text:
Edit-config for augment

having this augment to ietf-interfaces
module def-interfaces {
  namespace "xmlns=http://www.advaoptical.com/ns/def-interfaces";
  prefix def;

  import ietf-interfaces {
    prefix if;
  }

  augment "/if:interfaces/if:interface" {
    container interface-config {
      leaf owner-tag {
        type string;
      }
    }
  }
}

after sending the following edit-config
<rpc message-id="101"
  xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
  <edit-config xmlns:nc="urn:ietf:params:xml:ns:netconf:base:1.0">
    <target>
      <running/>
    </target>
    <config>
    <interfaces xmlns="urn:ietf:params:xml:ns:yang:ietf-interfaces" nc:operation="merge">
          <interface nc:operation="merge">
            <name>ip-4</name>
            <description>descr_ip-1</description>
            <type>ethernetCsmacd</type>
            <interface-config xmlns="http://www.advaoptical.com/ns/def-interfaces">
             <owner-tag>my interface</owner-tag>
           </interface-config>
          </interface>
        </interfaces>
    </config>
  </edit-config>
</rpc>

owner-tag leaf is not created. Netopeer sets only the following paths
[INF] (rp_dt_set_item_wrapper:559) Set item request running datastore, xpath: /ietf-interfaces:interfaces/interface[name='ip-4']
[INF] (rp_dt_set_item_wrapper:559) Set item request running datastore, xpath: /ietf-interfaces:interfaces/interface[name='ip-4']/description
[INF] (rp_dt_set_item_wrapper:559) Set item request running datastore, xpath: /ietf-interfaces:interfaces/interface[name='ip-4']/type

Get-config request +response with missing leaf
<?xml version="1.0" encoding="UTF-8"?>
 <rpc message-id="38" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
   <get-config xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
     <source>
       <running/>
     </source>
     <filter>
      <interfaces xmlns="urn:ietf:params:xml:ns:yang:ietf-interfaces">
	  <interface>
		<name>ip-4</name>
	  </interface>
       </interfaces>
     </filter>
   </get-config>
 </rpc>

#329
<rpc-reply message-id="38" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0"><data xmlns="urn:ietf:params:xml:ns:netconf:base:1.0"><interfaces xmlns="urn:ietf:params:xml:ns:yang:ietf-interfaces"><interface><name>ip-4</name><description>descr_ip-1</description><type>ethernetCsmacd</type></interface></interfaces></data></rpc-reply>
##

Hi
I'm using sysrepod 0.4.2, libyang 0.10.219, libnetconf2 0.7.35, Netopeer2 2.0.27 on a embedded system mips based.
I'm facing a similar problem with my augmented yang files.
The NETCONF manager sends
netopeer2-server[3578]: Session 1: received message:

4.4.4.4

Anyway the transaction doesn't close because of the following error message taken from the netopeer2-server output:
netopeer2-server[3578]: (cl_request_process:416) Sending session-refresh request.
netopeer2-server[3578]: (cl_request_process:438) session-refresh request sent, waiting for response.
netopeer2-server[3578]: (cl_request_process:460) session-refresh response received, processing.
netopeer2-server[3578]: EDIT_CONFIG: leaf /tiesse:set/tiesse-eth:eth1/ipaddr, operation 1
netopeer2-server[3578]: (cl_request_process:416) Sending set-item request.
netopeer2-server[3578]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[3578]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[3578]: EDIT_CONFIG: success (/tiesse:set/tiesse-eth:eth1/ipaddr).
netopeer2-server[3578]: (cl_request_process:416) Sending commit request.
netopeer2-server[3578]: (cl_request_process:438) commit request sent, waiting for response.
netopeer2-server[3578]: (cl_request_process:460) commit response received, processing.
netopeer2-server[3578]: (sr_commit:1905) Commit operation failed with 0 error(s).
netopeer2-server[3578]: DICT: inserting "Request could not be completed because the requested operation failed for a non-specific reason." with collision
netopeer2-server[3578]: DICT: inserting "en" with collision
netopeer2-server[3578]: DICT: inserting "An operation failed"
netopeer2-server[3578]: DICT: inserting "en" with collision
netopeer2-server[3578]: (cl_request_process:416) Sending discard-changes request.
netopeer2-server[3578]: (cl_request_process:438) discard-changes request sent, waiting for response.
netopeer2-server[3578]: (cl_request_process:460) discard-changes response received, processing.
netopeer2-server[3578]: Session 1: sending message:
at the same time sysrepod output is the following:
[DBG] (rp_get_changes_req_process:1609) Processing get changes request.
[DBG] (rp_dt_find_changes:221) Get changes: /tiesse:set/tiesse-eth:eth1//* limit:100 offset:1 cache hit
[DBG] (sr_cbuff_enqueue:467) Circular buffer enqueue to position=8, current count=1.
[DBG] (cm_msg_enqueue_cb:1657) New message enqueued into CM message queue.
[DBG] (sr_cbuff_dequeue:483) Circular buffer dequeue, new buffer head=9, count=0.
[DBG] (cm_conn_out_buff_flush:496) Sending 27 bytes of data.
[DBG] (cm_conn_out_buff_flush:502) 27 bytes of data sent.
[DBG] (cm_conn_read_cb:1050) fd 11 readable
[DBG] (cm_conn_read_cb:1063) 145 bytes of data received on fd 11
[DBG] (cm_conn_read_cb:1073) fd 11 would block
[DBG] (cm_conn_in_buff_process:1002) New message of size 141 bytes received.
[DBG] (sr_cbuff_enqueue:467) Circular buffer enqueue to position=3, current count=1.
[DBG] (rp_msg_process:3031) Threads: active=1/4, 1 requests in queue
[DBG] (sr_cbuff_dequeue:483) Circular buffer dequeue, new buffer head=4, count=0.
[DBG] (rp_notification_ack_process:2337) Notification ACK received with result = 3.
[ERR] (rp_notification_ack_process:2355) '/tiesse:set/tiesse-eth:eth1//' subscriber returned and error by processing of verify event: Item not found.
[ERR] (np_commit_notification_ack:994) Verifier for '/tiesse:set/tiesse-eth:eth1//' returned an error (msg: '(null)', xpath: '(null)'), commit will be aborted.
[DBG] (np_commit_notifications_complete:1051) Commit id=259953484 notifications complete.
[DBG] (rp_resume_commit:3075) Commit context in state 6
[INF] (rp_resume_commit:3080) Resuming commit with id 259953484 continue with abort
sysrepo-plugind instead seems to have properly handled the message and taken the right action
========== CHANGES: =============================================
[DBG] (cl_request_process:416) Sending get changes request.
[DBG] (cl_request_process:438) get changes request sent, waiting for response.
[DBG] (cl_request_process:460) get changes response received, processing.
[DBG] (change_value:278) xpath: /tiesse:set/tiesse-eth:eth1/ipaddr
[DBG] (sysrepo_str_value:789) /tiesse:set/tiesse-eth:eth1/ipaddr = '4.4.4.4'
[DBG] (change_value:282) cli_value: 4.4.4.4
MODIFIED: set
eth1
set eth1 ipaddr 4.4.4.4
[DBG] (cl_request_process:416) Sending get changes request.
[DBG] (cl_request_process:438) get changes request sent, waiting for response.
[DBG] (cl_request_process:460) get changes response received, processing.
[DBG] (sr_get_change_next:2545) All items has been read for xpath '/tiesse:set/tiesse-eth:eth1//*'
========== END OF CHANGES =======================================
[DBG] (module_change_cb:439) tiesse-ethernet callback return 0
[DBG] (cl_sm_conn_out_buff_flush:397) Sending 145 bytes of data.
[DBG] (cl_sm_conn_out_buff_flush:403) 145 bytes of data sent.
From sysrepo-plugind's point of view everything worked fine. Unfortunately the transaction couldn't be committed cause of the problems signalled by sysrepod/netopeer2-server
I want to remark that this edit-command worked fine prior the devel to master merge.
I haven't modified any of my custom sysrepo custom plugins in the meantime
best regards
fabio

They seem to be different issues, Fabio please create a separate issue.

skipping <interface-config> is correct because the module namespace is xmlns=http://www.advaoptical.com/ns/def-interfaces while the namespace of the <interface-config> is http://www.advaoptical.com/ns/def-interfaces. I had to run debugger to notice that :)

BTW, Fabio, for the first sight, your issues seems to be more connected with sysrepo and, in 0.4 introduced, verification callbacks.

I do not understand your explanation.
Are you saying it is that there is a mistake in the edit-config request?
If so which line is not correct, and what should it be?
the two namesapces look the  same to me
xmlns=http://www.advaoptical.com/ns/def-interfaces
http://www.advaoptical.com/ns/def-interfaces.

ip-4
descr_ip-1
ethernetCsmacd

my interface

another example where I get an rpc-ok on edit-config , but get nothing back on get for augmented module:
[2016/10/14 12:16:20.574295, 3] ssh_packet_socket_callback:  packet: read type 94 [len=1404,padding=9,comp=1394,payload=1394]
[2016/10/14 12:16:20.574360, 3] ssh_packet_process:  Dispatching handler for packet type 94
[2016/10/14 12:16:20.574391, 3] channel_rcv_data:  Channel receiving 1385 bytes data in 0 (local win=1256412 remote win=39566301)
[2016/10/14 12:16:20.574415, 3] channel_default_bufferize:  placing 1385 bytes into channel buffer (stderr=0)
[2016/10/14 12:16:20.574573, 3] channel_rcv_data:  Channel windows are now (local win=1255027 remote win=39566301)
[2016/10/14 12:16:20.574606, 3] ssh_channel_read_timeout:  Read (1) buffered : 1385 bytes. Window: 1255027
[2016/10/14 12:16:20.574631, 3] ssh_channel_read_timeout:  Read (1) buffered : 1384 bytes. Window: 1255027
[2016/10/14 12:16:20.574657, 3] ssh_channel_read_timeout:  Read (1) buffered : 1383 bytes. Window: 1255027
[2016/10/14 12:16:20.574682, 3] ssh_channel_read_timeout:  Read (1) buffered : 1382 bytes. Window: 1255027
[2016/10/14 12:16:20.574713, 3] ssh_channel_read_timeout:  Read (1) buffered : 1381 bytes. Window: 1255027
[2016/10/14 12:16:20.574738, 3] ssh_channel_read_timeout:  Read (1) buffered : 1380 bytes. Window: 1255027
[2016/10/14 12:16:20.574763, 3] ssh_channel_read_timeout:  Read (1) buffered : 1379 bytes. Window: 1255027
[2016/10/14 12:16:20.574790, 3] ssh_channel_read_timeout:  Read (1374) buffered : 1378 bytes. Window: 1255027
[2016/10/14 12:16:20.574817, 3] ssh_channel_read_timeout:  Read (1) buffered : 4 bytes. Window: 1255027
[2016/10/14 12:16:20.574841, 3] ssh_channel_read_timeout:  Read (1) buffered : 3 bytes. Window: 1255027
[2016/10/14 12:16:20.574867, 3] ssh_channel_read_timeout:  Read (1) buffered : 2 bytes. Window: 1255027
[2016/10/14 12:16:20.574891, 3] ssh_channel_read_timeout:  Read (1) buffered : 1 bytes. Window: 1255027
netopeer2-server[13211]: Session 1: received message:

<if:interfaces xmlns:if="urn:ietf:params:xml:ns:yang:ietf-interfaces" xmlns:ianaift="urn:ietf:params:xml:ns:yang:iana-if-type" xmlns:inet="urn:ietf:params:xml:ns:yang:ietf-inet-types" xmlns="http://www.advaoptical.com/ns/adva-ensemble-interfaces-ip" xmlns:nc="urn:ietf:params:xml:ns:netconf:base:1.0" nc:operation="merge">
if:interface
if:nametun-1</if:name>
if:descriptiondescr_tun-1</if:description>
if:typeianaift:ethernetCsmacd</if:type>

int-tun
abcd

ipsec-128
3.4.5.6
45

</if:interface>
</if:interfaces>
</config>

netopeer2-server[13211]: DICT: inserting "rpc" with collision
netopeer2-server[13211]: DICT: inserting "message-id" with collision
netopeer2-server[13211]: DICT: inserting "44" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:netconf:base:1.0"
netopeer2-server[13211]: DICT: inserting (refcount) "edit-config"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:netconf:base:1.0"
netopeer2-server[13211]: DICT: inserting (refcount) "target"
netopeer2-server[13211]: DICT: inserting (refcount) "candidate"
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) "config"
netopeer2-server[13211]: DICT: inserting (refcount) "interfaces"
netopeer2-server[13211]: DICT: inserting (refcount) "if"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:yang:ietf-interfaces"
netopeer2-server[13211]: DICT: inserting (refcount) "ianaift"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:yang:iana-if-type"
netopeer2-server[13211]: DICT: inserting (refcount) "inet"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:yang:ietf-inet-types"
netopeer2-server[13211]: DICT: inserting "http://www.advaoptical.com/ns/adva-ensemble-interfaces-ip" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "nc"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:netconf:base:1.0"
netopeer2-server[13211]: DICT: inserting "operation" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "merge"
netopeer2-server[13211]: DICT: inserting (refcount) "interface"
netopeer2-server[13211]: DICT: inserting (refcount) "name"
netopeer2-server[13211]: DICT: inserting "tun-1" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "description"
netopeer2-server[13211]: DICT: inserting "descr_tun-1" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "type"
netopeer2-server[13211]: DICT: inserting "ianaift:ethernetCsmacd" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "interface-config"
netopeer2-server[13211]: DICT: inserting (refcount) "http://www.advaoptical.com/ns/adva-ensemble-interfaces"
netopeer2-server[13211]: DICT: inserting (refcount) "nc"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:netconf:base:1.0"
netopeer2-server[13211]: DICT: inserting (refcount) "operation"
netopeer2-server[13211]: DICT: inserting (refcount) "merge"
netopeer2-server[13211]: DICT: inserting (refcount) "interface-type"
netopeer2-server[13211]: DICT: inserting (refcount) "int-tun"
netopeer2-server[13211]: DICT: inserting (refcount) "owner-tag"
netopeer2-server[13211]: DICT: inserting "abcd" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "tunnel"
netopeer2-server[13211]: DICT: inserting (refcount) "http://www.advaoptical.com/ns/adva-ensemble-interfaces-tunnel"
netopeer2-server[13211]: DICT: inserting (refcount) "operation"
netopeer2-server[13211]: DICT: inserting (refcount) "merge"
netopeer2-server[13211]: DICT: inserting (refcount) "type"
netopeer2-server[13211]: DICT: inserting (refcount) "ipsec-128"
netopeer2-server[13211]: DICT: inserting (refcount) "dest-ip"
netopeer2-server[13211]: DICT: inserting "3.4.5.6" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "tunnel-id"
netopeer2-server[13211]: DICT: inserting "45" with collision
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) "merge"
netopeer2-server[13211]: DICT: inserting (refcount) "test-then-set"
netopeer2-server[13211]: DICT: inserting (refcount) "stop-on-error"
netopeer2-server[13211]: Resolving unresolved data nodes and their constraints...
netopeer2-server[13211]: All data nodes and constraints resolved.
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:edit-config/target/*":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:edit-config"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "target"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "*"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "edit-config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[25]
netopeer2-server[13211]: DICT: inserting (refcount) "target"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[26]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[32]
netopeer2-server[13211]: DICT: inserting (refcount) "*"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[33]
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:edit-config/default-operation":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:edit-config"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "default-operation"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "edit-config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[25]
netopeer2-server[13211]: DICT: inserting (refcount) "default-operation"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[26]
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:edit-config/test-option":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:edit-config"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "test-option"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "edit-config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[25]
netopeer2-server[13211]: DICT: inserting (refcount) "test-option"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[26]
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:edit-config/error-option":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:edit-config"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "error-option"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "edit-config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[25]
netopeer2-server[13211]: DICT: inserting (refcount) "error-option"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[26]
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:edit-config/config":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:edit-config"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "config"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "edit-config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[25]
netopeer2-server[13211]: DICT: inserting (refcount) "config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[26]
netopeer2-server[13211]: DICT: inserting "iana-if-type:ethernetCsmacd" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "int-tun"
netopeer2-server[13211]: DICT: inserting "ianaift:ethernetCsmacd" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "int-tun"
netopeer2-server[13211]: EDIT_CONFIG: ds 8270720, defop 1, testopt 0, config:

tun-1
descr_tun-1
ianaift:ethernetCsmacd

int-tun
abcd

ipsec-128
3.4.5.6
45

netopeer2-server[13211]: EDIT_CONFIG: list /ietf-interfaces:interfaces/interface[name='tun-1'], operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/description, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/description).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/type, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/type).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/interface-type, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/interface-type).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/owner-tag, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/owner-tag).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/adva-ensemble-interfaces-tunnel:tunnel/type, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/adva-ensemble-interfaces-tunnel:tunnel/type).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/adva-ensemble-interfaces-tunnel:tunnel/dest-ip, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/adva-ensemble-interfaces-tunnel:tunnel/dest-ip).
netopeer2-server[13211]: EDIT_CONFIG: leaf /ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/adva-ensemble-interfaces-tunnel:tunnel/tunnel-id, operation 1
netopeer2-server[13211]: (cl_request_process:416) Sending set-item request.
netopeer2-server[13211]: (cl_request_process:438) set-item request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) set-item response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: success (/ietf-interfaces:interfaces/interface[name='tun-1']/adva-ensemble-interfaces:interface-config/adva-ensemble-interfaces-tunnel:tunnel/tunnel-id).
netopeer2-server[13211]: (cl_request_process:416) Sending validate request.
netopeer2-server[13211]: (cl_request_process:438) validate request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) validate response received, processing.
netopeer2-server[13211]: (sr_validate:1844) Validate operation failed with 1 error(s).
netopeer2-server[13211]: (cl_request_process:416) Sending discard-changes request.
netopeer2-server[13211]: (cl_request_process:438) discard-changes request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) discard-changes response received, processing.
netopeer2-server[13211]: EDIT_CONFIG: done.
netopeer2-server[13211]: Session 1: sending message:
#92
[2016/10/14 12:16:20.615387, 3] ssh_socket_unbuffered_write:  Enabling POLLOUT for socket
[2016/10/14 12:16:20.616177, 3] packet_send2:  packet: wrote [len=28,padding=13,comp=14,payload=14]
[2016/10/14 12:16:20.616315, 3] channel_write_common:  channel_write wrote 5 bytes
netopeer2-server[13211]: Session 1: sending message:

[2016/10/14 12:16:20.616739, 3] packet_send2:  packet: wrote [len=108,padding=6,comp=101,payload=101]
[2016/10/14 12:16:20.617119, 3] channel_write_common:  channel_write wrote 92 bytes
[2016/10/14 12:16:20.617261, 3] ssh_socket_unbuffered_write:  Enabling POLLOUT for socket
netopeer2-server[13211]: Session 1: sending message:

[2016/10/14 12:16:20.618246, 3] packet_send2:  packet: wrote [len=28,padding=14,comp=13,payload=13]
[2016/10/14 12:16:20.618502, 3] channel_write_common:  channel_write wrote 4 bytes
[2016/10/14 12:16:20.619159, 3] ssh_socket_unbuffered_write:  Enabling POLLOUT for socket
[2016/10/14 12:20:21.586177, 3] ssh_packet_socket_callback:  packet: read type 94 [len=396,padding=10,comp=385,payload=385]
[2016/10/14 12:20:21.586235, 3] ssh_packet_process:  Dispatching handler for packet type 94
[2016/10/14 12:20:21.586264, 3] channel_rcv_data:  Channel receiving 376 bytes data in 0 (local win=1254651 remote win=39566048)
[2016/10/14 12:20:21.586288, 3] channel_default_bufferize:  placing 376 bytes into channel buffer (stderr=0)
[2016/10/14 12:20:21.586319, 3] channel_rcv_data:  Channel windows are now (local win=1254275 remote win=39566048)
[2016/10/14 12:20:21.586351, 3] ssh_channel_read_timeout:  Read (1) buffered : 376 bytes. Window: 1254275
[2016/10/14 12:20:21.586376, 3] ssh_channel_read_timeout:  Read (1) buffered : 375 bytes. Window: 1254275
[2016/10/14 12:20:21.586402, 3] ssh_channel_read_timeout:  Read (1) buffered : 374 bytes. Window: 1254275
[2016/10/14 12:20:21.586426, 3] ssh_channel_read_timeout:  Read (1) buffered : 373 bytes. Window: 1254275
[2016/10/14 12:20:21.586450, 3] ssh_channel_read_timeout:  Read (1) buffered : 372 bytes. Window: 1254275
[2016/10/14 12:20:21.586474, 3] ssh_channel_read_timeout:  Read (1) buffered : 371 bytes. Window: 1254275
[2016/10/14 12:20:21.586501, 3] ssh_channel_read_timeout:  Read (366) buffered : 370 bytes. Window: 1254275
[2016/10/14 12:20:21.586647, 3] ssh_channel_read_timeout:  Read (1) buffered : 4 bytes. Window: 1254275
[2016/10/14 12:20:21.586673, 3] ssh_channel_read_timeout:  Read (1) buffered : 3 bytes. Window: 1254275
[2016/10/14 12:20:21.586699, 3] ssh_channel_read_timeout:  Read (1) buffered : 2 bytes. Window: 1254275
[2016/10/14 12:20:21.586723, 3] ssh_channel_read_timeout:  Read (1) buffered : 1 bytes. Window: 1254275
netopeer2-server[13211]: Session 1: received message:

</filter>

netopeer2-server[13211]: DICT: inserting "rpc" with collision
netopeer2-server[13211]: DICT: inserting "message-id" with collision
netopeer2-server[13211]: DICT: inserting "46" with collision
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:netconf:base:1.0"
netopeer2-server[13211]: DICT: inserting (refcount) "get-config"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:netconf:base:1.0"
netopeer2-server[13211]: DICT: inserting (refcount) "source"
netopeer2-server[13211]: DICT: inserting (refcount) "candidate"
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) "filter"
netopeer2-server[13211]: DICT: inserting (refcount) "interfaces"
netopeer2-server[13211]: DICT: inserting (refcount) "urn:ietf:params:xml:ns:yang:ietf-interfaces"
netopeer2-server[13211]: DICT: inserting "
      " with collision
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: DICT: inserting (refcount) ""
netopeer2-server[13211]: Resolving unresolved data nodes and their constraints...
netopeer2-server[13211]: All data nodes and constraints resolved.
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:get-config/source/*":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:get-config"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "source"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "*"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "get-config"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[24]
netopeer2-server[13211]: DICT: inserting (refcount) "source"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[25]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[31]
netopeer2-server[13211]: DICT: inserting (refcount) "*"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[32]
netopeer2-server[13211]: (cl_request_process:416) Sending session-switch-ds request.
netopeer2-server[13211]: (cl_request_process:438) session-switch-ds request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) session-switch-ds response received, processing.
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:*/filter":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:*"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "filter"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "*"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[15]
netopeer2-server[13211]: DICT: inserting (refcount) "filter"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[16]
netopeer2-server[13211]: XPATH: expression "/ietf-netconf:*/ietf-netconf-with-defaults:with-defaults":
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf:*"
netopeer2-server[13211]: XPATH:	Token Operator(Path), in expression "/"
netopeer2-server[13211]: XPATH:	Token NameTest, in expression "ietf-netconf-with-defaults:with-defaults"
netopeer2-server[13211]: XPATH: eval_absolute_location_path parsed Operator(Path)[0]
netopeer2-server[13211]: DICT: inserting (refcount) "*"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[1]
netopeer2-server[13211]: XPATH: eval_relative_location_path parsed Operator(Path)[15]
netopeer2-server[13211]: DICT: inserting (refcount) "with-defaults"
netopeer2-server[13211]: XPATH: eval_node_test              parsed NameTest[16]
netopeer2-server[13211]: (cl_request_process:416) Sending session-refresh request.
netopeer2-server[13211]: (cl_request_process:438) session-refresh request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) session-refresh response received, processing.
netopeer2-server[13211]: (cl_request_process:416) Sending get-items request.
netopeer2-server[13211]: (cl_request_process:438) get-items request sent, waiting for response.
netopeer2-server[13211]: (cl_request_process:460) get-items response received, processing.
netopeer2-server[13211]: (sr_get_items:870) Error by processing of the request.
netopeer2-server[13211]: Session 1: sending message:
#142
[2016/10/14 12:20:21.595751, 3] ssh_socket_unbuffered_write:  Enabling POLLOUT for socket
[2016/10/14 12:20:21.595792, 3] packet_send2:  packet: wrote [len=28,padding=12,comp=15,payload=15]
[2016/10/14 12:20:21.595817, 3] channel_write_common:  channel_write wrote 6 bytes
netopeer2-server[13211]: Session 1: sending message:

[2016/10/14 12:20:21.595893, 3] packet_send2:  packet: wrote [len=156,padding=4,comp=151,payload=151]
[2016/10/14 12:20:21.595919, 3] channel_write_common:  channel_write wrote 142 bytes
[2016/10/14 12:20:21.595950, 3] ssh_socket_unbuffered_write:  Enabling POLLOUT for socket
netopeer2-server[13211]: Session 1: sending message:

[2016/10/14 12:20:21.596018, 3] packet_send2:  packet: wrote [len=28,padding=14,comp=13,payload=13]
[2016/10/14 12:20:21.596043, 3] channel_write_common:  channel_write wrote 4 bytes
[2016/10/14 12:20:21.596072, 3] ssh_socket_unbuffered_write:  Enabling POLLOUT for socket

Radek
I have opened a new issue on sysrepo
thanks
fabio
On 14/10/2016 17:30, Radek Krejčí wrote:

BTW, Fabio, for the first sight, your issues seems to be more
connected with sysrepo and, in 0.4 introduced, verification callbacks.
—
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Line 13 In the edit-config is wrong, according to the schema it is supposed to be:
<interface-config xmlns="xmlns=http://www.advaoptical.com/ns/def-interfaces">

but I guess that you want rather change the namespace of the module to:
module def-interfaces {
  namespace "http://www.advaoptical.com/ns/def-interfaces";

This is the namespace of the module:
module def-interfaces {
namespace "http://www.advaoptical.com/ns/def-interfaces";
prefix defif;
isn't line 13 suppose to be the namespace of the module?
this is the actual xml request I sent:

What I see in the first comment is different, and that is what I have used for testing. I'm going to try it again with the correct namespace in the module.

btw, please post the code as code listings, not as images, it is hardly usable for anything

with the correct namespace, everything is working as expected, so I'm closing the issue. Used schema and edit config is below.
def-interfaces.yang:
module def-interfaces {
  namespace "http://www.advaoptical.com/ns/def-interfaces";
  prefix def;

  import ietf-interfaces {
    prefix if;
  }

  augment "/if:interfaces/if:interface" {
    container interface-config {
      leaf owner-tag {
        type string;
      }
    }
  }
}

rpc:
<rpc xmlns="urn:ietf:params:xml:ns:netconf:base:1.0" message-id="17">
  <edit-config xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
    <target><running/></target>
    <default-operation>merge</default-operation>
    <test-option>test-then-set</test-option>
    <error-option>stop-on-error</error-option>
    <config>
      <interfaces xmlns:nc="urn:ietf:params:xml:ns:netconf:base:1.0" xmlns="urn:ietf:params:xml:ns:yang:ietf-interfaces" nc:operation="merge">
        <interface nc:operation="merge">
          <name>ip-4</name>
          <description>descr_ip-1</description>
          <type>ethernetCsmacd</type>
          <interface-config xmlns="http://www.advaoptical.com/ns/def-interfaces">
            <owner-tag>my interface</owner-tag>
          </interface-config>
        </interface>
      </interfaces>
    </config>
  </edit-config>
</rpc>

authors: fabioantonini joanlandry lukasmacko rkrejci


text:
issues in netopeera2 cross compilaton issues

Hi MIchalvasco,
i am trying to build netopeera2 (git file ) on x86 64bit  architecture ,little endian & ubuntu operating system.
Doing arm cross compilations on it.
i am getting issues in /path/netopeera2/build/sudo cmake ..
i am getting following errors.
-- Unable to learn libnetconf2 thread support, check skipped
-- Check if the system is big endian
-- Searching 16 bit integer
CMake Error at /usr/share/cmake-3.10/Modules/TestBigEndian.cmake:49 (message):
no suitable type found
Call Stack (most recent call first):
CMakeModules/UseCompat.cmake:20 (TEST_BIG_ENDIAN)
CMakeLists.txt:171 (use_compat)
-- Configuring incomplete, errors occurred!
Regards
Syam

Could you please look at the actual error? It most likely has nothing to do with anything that was printed. Should be in CMakeError.txt or something like that.

source: gharchive/issue

authors: michalvasko syamkumarv

license_type: permissive

license_source: github-api


text:
Nacm authorization issue

Hi I am getting Nacm permission denied, What could be the reason I have set all permission correctly in Nacm I hope
> edit-config  --target running --config --defop replace

Replace with below XML's
<users xmlns="urn:o-ran:user-mgmt:1.0"  >
 <user>
   	<name>oranuser</name>
   	<account-type>PASSWORD</account-type>
   	<password>oranuser</password>
   	<enabled>true</enabled>
 </user>
 <user>
      <name>Samueljohn</name>
      <password>admin123</password>
 	<account-type>PASSWORD</account-type>
<enabled>true</enabled>
   </user>
   <user>
       <name>Samueljohnj</name>
       <password>admin123</password>
 	 <account-type>PASSWORD</account-type>
       <enabled>true</enabled>
   </user>
   <user>
       <name>Samueljohnjj</name>
       <password>wireless123</password>
 	 <account-type>PASSWORD</account-type>
       <enabled>true</enabled>
   </user>
</users>

ERROR
	type:     protocol
	tag:      access-denied
	severity: error
	path:     /o-ran-usermgmt:users/user
	message:  Access to the data model "o-ran-usermgmt" is denied because "Samueljohn" NACM authorization failed.

SYSTEM LOGS
Nov  4 07:02:52 mcel daemon.err netopeer2-server[2021]: Access to the data model "o-ran-usermgmt" is denied because "Samueljohn" NACM authorization fai.
Nov  4 07:02:52 mcel daemon.info netopeer2-server[2021]: Failed processing of "rpc" event with ID 8 priority 0 (remaining 1 subscribers).
Nov  4 07:02:52 mcel daemon.err netopeer2-server[2021]: Access to the data model "o-ran-usermgmt" is denied because "Samueljohn" NACM authorization fai.

NACM permissions are given as
<rule>
            <name>o-ran-usermgmt-permission1</name>
            <module-name>o-ran-usermgmt</module-name>
            <path xmlns:o-ran-usermgmt="urn:o-ran:user-mgmt:1.0">/o-ran-usermgmt:users/o-ran-usermgmt:user/o-ran-usermgmt:name</path>
            <access-operations>create read update delete</access-operations>
            <action>permit</action>
        </rule>
        <rule>
            <name>o-ran-usermgmt-permission2</name>
            <module-name>o-ran-usermgmt</module-name>
            <path xmlns:o-ran-usermgmt="urn:o-ran:user-mgmt:1.0">/o-ran-usermgmt:users/o-ran-usermgmt:user/o-ran-usermgmt:account-type</path>
            <access-operations>create read update delete</access-operations>
            <action>permit</action>
        </rule>
        <rule>
            <name>o-ran-usermgmt-permission3</name>
            <module-name>o-ran-usermgmt</module-name>
            <path xmlns:o-ran-usermgmt="urn:o-ran:user-mgmt:1.0">/o-ran-usermgmt:users/o-ran-usermgmt:user/o-ran-usermgmt:password</path>
            <access-operations>create update delete</access-operations>
            <action>permit</action>
        </rule>
        <rule>
            <name>o-ran-usermgmt-permission4</name>
            <module-name>o-ran-usermgmt</module-name>
            <path xmlns:o-ran-usermgmt="urn:o-ran:user-mgmt:1.0">/o-ran-usermgmt:users/o-ran-usermgmt:user/o-ran-usermgmt:enabled</path>
            <access-operations>create read update delete</access-operations>
            <action>permit</action>
        </rule>
        <rule>

Can you tell me where I went wrong or is this a bug?

Hi @michalvasko  can you help out here?

Please be patient, I see all the issues but there are lots of them and I have other actual work, too.
Based on the error
path:     /o-ran-usermgmt:users/user

you need to grant access to user as well, the paths always target specific nodes.

Oh thank you for your kind comments and your quick response I will check and get back to you.


text:
Добавить гитигнор

На гитхаб не нужно выкладывать логи игры, результаты компиляции и т.п.

Добавил

repo: CHEYSOFF/PACMAN

license: MIT


text:
Can't place slabs next to each other without first completing the block

Hey there! First off, thanks for your time and effort that's gone into the mod :)
I've just started using the mod and when I try to place oak slabs one beside another by right clicking the side of a slab while holding another (building a 1/2 block floor), I end up placing the slab above/below the one I've clicked on.. Is it not possible to place slabs using the sides of other slabs while this mod is installed, or am I missing something? I've gone through the in-game controls, checked my configs and tried shift+right-clicking on the slabs.. no luck.

I'm having the same issue, when you're making a slab floor, it's enough to drive you bonkers.
This is a really cool mod idea, and I'm very reluctant to give it up because of this quirk, so right now I'm doing a lot of stuff with scaffolding to work around it. I'd rather it Just Worked though ;)

I believe Vanilla uses raytracing to determine at what angle you're clicking on the block to decide if you need to put a slab on the side or make a doubleslab or whatever. You could look into this?

Sorry for the delay, I'm looking into this issue and suspect it is something to do with how I ported the 1.12 version to 1.14 (assuming this is on the 1.14 version). What I suspect is, as you can place slabs on top of a slab by clicking on the side of the block, I have accidentally forgot to check whether you intend to place it on the side of the block or the top. I'll try to get this fixed as soon as possible, again sorry for the delay

This should now be fixed in the latest version, if you have any more issues, be sure to let me know!

I found out this can still happen if the upper half of a slab is right-clicked to placed another slab above. It'll instead make the block below into a double slab.


text:
🛑 Kanboard is down

In d6c55e2, Kanboard (https://kb.m5e.de) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Kanboard is back up in 6d3f23c.

repo: CMiksche/status


text:
Build issues (undefined symbol: cblas_ctrmv)

Following build instructions per the README.md, on intel linux with cargo 1.80.1-nightly (376290515 2024-07-16):
git clone git@github.com:COMBINE-lab/TreeTerminus.git
cd TreeTerminus
cargo build --release

initially gives an error: error[E0635]: unknown feature "proc_macro_span_shrink"
After deleting Cargo.lock and rebuilding, the process completes. However, target/release/treeterminus yields:
target/release/treeterminus: symbol lookup error: /lib64/libgsl.so.23: undefined symbol: cblas_ctrmv

Hi,
I apologize for the late reply. So it seems the issue is due to the inability of the program to find the libgsl library. Can you try installing the libgsl-dev and then compile? Also, can you mention the version of g++ ,  (g++ --version ).

authors: NPSDC sbresnahan

repo: COMBINE-lab/TreeTerminus


text:
v1-1 checklist

[x] Update raw data through end of June
[x] Add all old 1min and 5min data to raw
[x] Add all old redox data
[x] Test run v1.1 with redox and 1/5min data
[ ] New README

Hi @stephpenn1 a brief update -

As I mentioned yesterday, I was a little concerned about the timeline. But I cleared a things of my calendar and did a bunch of prep work and PRs and am feeling much better
I just finished a full test run of the v1-1 (data through end of June; 1min and 5min data included; redox included) and it went well. 206 million observations!
I'll take a close look at the test run outputs, and we have some things to nail down
Overall, however, I think we can produce a final v1-1 by a week from now so that you are able to submit to ESS-DIVE by end of the month

That is great news, thanks so much for your work on this

@stephpenn1 I am traveling the next couple days, doing a little Sunday work so things are ready for you tomorrow.
The v1-1 beta has been uploaded to the google drive for you to look through and check. Things for us to do:

[ ] Resolve questions to Roy in #175 and merge that PR
[ ] Carefully read the main README
[ ] I have spot-checked most of the new data (June and July 2024) but please feel free to do so as well
[ ] Anything else you see

When things look good to you and we have an up-to-date main I will regenerate, upload the final v1-1, and let you take it from there (although obv am happy to talk if useful). OK?

repo: COMPASS-DOE/data-workflows


text:
TEROS data in the test PTR-UP

...they're there in the raw data, the L1-normalize log says they're processed, but why don't they appear in the L1 output files? 😕

Checked and confirmed that data are present in test L1 outputs. I don't know what was going on above!

repo: COMPASS-DOE/sensor-data-pipeline


text:
Add standardise_mom6_filenames.sh script (#32)

This PR is related to https://github.com/COSIMA/om3-scripts/issues/32 and introduces a simple script for the automated postprocessing of MOM6 outputs. The script follows the agreed template, which can be referenced in https://github.com/COSIMA/access-om3/issues/190#issuecomment-2272409582.
Regarding WW3, it would be good to change the outputs once some changes to the wave cap by NorESM are merged. For more details, refer to https://github.com/COSIMA/access-om3/issues/190#issuecomment-2272615701

Hello @anton-seaice , could you please review it when you are available?

source: gharchive/pull-request


text:
Streamline double decomposition for alldiff

Alldiff has two decompositions: a set of pairwise variable disequalities, and a set of at-most-one constraints (one for each possible value of the values for the variables in the alldiff). Currently, the pairwise disequalities is used in decompose, the at-most-one constraints in linearize.
The pairwise disequalities have as advantage that they do not depend on the size of the domain: even for variables with large domains (say, 0..999999) the size of the decomposition remains quadratic (in the number of variables). The at-most-one has the advantage of a better linear relaxation if the integer variables will be converted to Boolean variables anyway. E.g., for the pigeonhole or sudoku problem, you very much prefer the at-most-one encoding when solving with an ILP solver (SAT solvers will decompose this at-most-one to the pairwise disequalities again).
A simple heuristic is to check the number of values in the domains of the variables. If it is larger than quadratic the number of variables, go for the pairwise disequalities decomposition. Otherwise, use the at-most-one.

This is probably part of the larger question of specializing decompositions of certain constraints for certain (types of) solvers.
For example, the current decomposition of Circuit is very inefficient for the Gurobi solver, probably because it uses AllDifferent constraints, as well as Element constraints!
But much better decompositions, specialized for MIP do exist such as the Miller-Tucker-Zemlin decomposition:
https://how-to.aimms.com/Articles/332/332-Miller-Tucker-Zemlin-formulation.html
The question is, how do we implement this in a clean way? Do it in linearize? Or should the decompose() function have an argument "type" which allows the caller to chose which decomposition to use?
Personally, I think linearize would be the best place to do it...

The above points open a more general discussion. Different decompositions are better for different types of solver. And this is constraint based. Thus, also the different decompositions should be done on the constraints classes, and not in linearize, if we decide to go with specializing decompositions of certain constraints for certain (types of) solvers. If this goes more than the Circuit constraint (and it should imo), it would not be clean to just have all in linearize.
We don't have to use a "type" argument in decompose which will not be so clean. I think that we can just have a decompose_linear(), function for decomposition in linearize. This will just call decompose() by default in the GlobalConstraint class, unless otherwise specified. Thus, for constraints that we find a better decomposition, we can implement the decompose_linear() function. Then linearize will call decompose_linear() instead of decompose().

authors: Dimosts IgnaceBleukx JoD

repo: CPMpy/cpmpy


text:
Application properties

Using/Injecting value from application.properties with Spring and Spring Boot

We decided to use the load method because we couldn't retrieve any value using the spring boot build method from an application's properties file.


text:
feat!: Disallow nonlocal value edges into FuncDefn's

Closes #936
Sorry if this is a bit rough - was a bit rushed. It'd be great to have a test for dom edges too.
BREAKING CHANGE: Hugr's with nonlocal ("Inter-Graph") edges that enter FuncDefns will now fail validation

I fiddled the order of things so that if you have an edge that enters just a FuncDefn, you'll get the "no edge into funcdefn" error; previously you'd have got the "missing order edge" error (and you can't actually add the order edge to the funcdefn, as you would need to do to get the "no edge into funcdefn" error, because funcdefns can't receive order edges).
The test for that can't be constructed with the builder (because the builder always tries to add the order edge, and fails), so would have to duplicate most of test_ext_edge. Which doesn't feel worth it to check we've slightly-improved an error message :(. I'm hoping this way is acceptable for being simpler anyway :)...

repo: CQCL/hugr


text:
Get menu information from dan, and design the menu

Linking which ingredients are used in each menu item.

6 standard frappys min
12 ingredients min
Must include Macha

Frappuccinos:

Pumpkin Spice
Caramel
Mocha Cookie Crumble
Macha
Vanilla Bean
The Diabetes Special

Ingredients:
Milks:
- Milk
- Soy Milk
Base:
- Coffee
- Cream
Extras:
- Secret Sauce
- Vanilla
- Caramel
- Pumpkin Sauce
- Mocha
- Macha
- Chocolate
- Oreos
- Sugar

Ingredient List for Frappe's
Pumpkin Spice

Soy Milk
Coffee
Pumpkin Sauce x2
Sugar
Whip Cream

Caramel

Coffee
Milk
Caramel x2
Sugar
Whip Cream

Mocha Cookie Crumble

Milk
Cream
Secret Sauce
Oreos
Whip Cream

Macha

Soy Milk
Cream
Macha x3

Vanilla Bean

Soy Milk
Coffee
Vanilla x3
Chocolate Drizzle x2
Whip Cream

The Diabetes Special

Milk
Cream
Secret Sauce x3
Vanilla
Caramel
Pumpkin Sauce x2
Mocha
Macha x2
Chocolate Drizzle x3
Oreos
Sugar x4
Whip Cream

Fixed in latest release, now just reload the database

authors: SeaCastle dalyndalton

license: Unlicense


text:
kohchihao.adoc: Add order done

In this PR,

I added order done to my PPP

https://github.com/kohchihao/main/blob/chihao-ppp-update/docs/team/kohchihao.adoc

Pull Request Test Coverage Report for Build 384

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 87.873%

Totals

Change from base Build 380:
0.0%

Covered Lines:
2884

Relevant Lines:
3282

💛  - Coveralls

authors: coveralls kohchihao


text:
Review: I see no nodes / Http_CreateRequestFailed

Describe the bug
When attempting to create nodes I'm getting this exception: Http_CreateRequestFailed
Note while I started with the install instructions as they are at: https://csbiology.github.io/FSharpGephiStreamer/exampleAnalysis.html I made some adjustments. What you're currently doing:
let addOboNode (node:GONode) =

    let nodeConverter (node:GONode) =
        [
            Grammar.Attribute.Label (sprintf "%s | %s {%s}" node.Id node.TermDescription node.NameSpace);
            Grammar.Attribute.Size  10.;
            Grammar.Attribute.Color node.Color;
            Grammar.Attribute.UserDef ("UserData",node.TermDescription);
        ]
    Streamer.addNode nodeConverter node.Id node

goNodes |> List.map addOboNode

means that you're masking errors with the implicit ignore on the List.map (which generates warnings). I suggest you need to choose, if you're going to use the Either monad then it's important to include that in your examples
As to the actual error, I do have Gephi running but perhaps there's an access issue? Any guidance on debugging this?
Expected behavior
Nodes and edges into Gephi
OS and framework information (please complete the following information):

OS: Windows 10
.Net core SDK version [e.g. 2.2.203 ]

Additional context
This is possibly related to #15 perhaps I have the wrong version for you?
https://github.com/openjournals/joss-reviews/issues/1445

The streamer sends the edge and node data to a local server created by the graph streaming plugin.
So additionally to #15 (the creation of the Json failing due to the missing Newtonsoft.Json dependency), i could imagine two problems that could cause this:

the streaming master server is not enabled :

We stream nodes and edges to the following workspace per default:
"http://localhost:8080/workspace1?operation=updateGraph" (workspace 1).
if you have workspaces with other names you can change the target url by using the setEnvironment function as seen here :

I have a hard time reproducing your error. I opened a new script and created the following dependency file in the same folder:
generate_load_scripts: true

source https://www.nuget.org/api/v2

nuget FSharpGephiStreamer

If i now create a script file with the generated loading script (main.group.fsx), and use the functions provided in the streaming docs:
#load @"C:\Users\Kevin\source\scripts\GephiStreamerTest\.paket\load\netstandard2.1\main.group.fsx"

open FSharpGephiStreamer

/// Record type that represents a custom node
type MyNode = {
    Id    : int
    Label : string
    Size  : float
    Data  : string
    }

/// Record type that represents a custom edge
type MyEdge = {
    Id :     int
    Source : int
    Target : int
    Weight : float
    }

///converts a MyNode type to a list of grammar attributes
let nodeConverter (node:MyNode) =
    [
        Grammar.Attribute.Label node.Label;
        Grammar.Attribute.Size  node.Size;
        Grammar.Attribute.Color (Colors.Table.StatisticalGraphics24.getRandomColor());
        Grammar.Attribute.UserDef ("UserData",node.Data);
    ]

///converts a MyEdge type to a list of grammar attributes
let edgeConverter (edge:MyEdge) =
    [
        Grammar.Attribute.Size  edge.Weight;
        Grammar.Attribute.EdgeType  Grammar.EdgeDirection.Undirected;
        Grammar.Attribute.Color Colors.Table.Office.grey ;
    ]

///Adds a node of type MyNode using the node converter to the gephi graph
let addMyNode (node:MyNode) =
    Streamer.addNode nodeConverter node.Id node

///Adds an edge of type MyEdge using the edge converter to the gephi graph
let addMyEdge (edge: MyEdge) =
    Streamer.addEdge edgeConverter edge.Id edge.Source edge.Target edge

let myNode = {Id = 1; Label = "FOO" ; Size = 4.; Data = "BAR"}

addMyNode myNode

I get a node in gephi with the current nuget package:
Before (Go to the data laboratory tab in gephi):

After running the script:

I'm still unable to see any nodes. When I tried the code specified above, I get the following error (I get the same error when I try the other example):
Exception thrown: 'System.NullReferenceException' in FSharpGephiStreamer.dll
Exception thrown: 'System.NullReferenceException' in System.Private.CoreLib.dll
I do see this in the console:
{"an":{"1":{"label":"FOO","size":4.0,"color":"#8DD593","UserData":"BAR"}}}
However I am still unable to see anything in Gephi.
I also verified that Gephi was the only process using ports 8080 and 8443.

@cgravill :

means that you're masking errors with the implicit ignore on the List.map (which generates warnings). I suggest you need to choose, if you're going to use the Either monad then it's important to include that in your examples

I added this to the new basic sample
Is this sufficient for you?

@PrashantVaidyanathan

I do see this in the console:
{"an":{"1":{"label":"FOO","size":4.0,"color":"#8DD593","UserData":"BAR"}}}

This means that the Json string is created successfully. The error must be happening somewhere around here in the source code:

    /// Adds a node to the gephi graph using the given node converters grammar attribute mapping
    let addNode (nodeConverter:NodeConverter<'node>) nodeId =
        let nodeId' = string nodeId
        (Either.tryCatch

            // This works for you

            (fun (node:'node) ->  (jsonFormatNode Action.Add nodeId' (nodeConverter node)))
            (fun exn  -> Error.CreateJsonFailed exn.Message))
        >> Either.bind (generatePostRequest (getEnvirmonment ()) )
        >> Either.bind evalHttpResponseText
        >> Either.either
            (fun _     -> Success nodeId' )

            //This fails

            (fun error -> Failure error )

However i find it strange that we get a null reference exception here. I uploaded a new package with updated dependencies, I hope this can fix your error.

I'm still getting a null reference exception (even with the updated dependencies). I think you are right, the error is occurring here:
let addMyNode (node:MyNode) =
    Streamer.addNode nodeConverter node.Id node
The specific error is:
Exception thrown: 'System.NullReferenceException' in FSharpGephiStreamer.dll ("Object reference not set to an instance of an object.")

are you sure you have the right package @PrashantVaidyanathan ? The nuget page lists 0 downloads for 1.1.2:

Yes. I'm not sure why the nuget page hasn't updated yet though.

I was finally able to reproduce the error, now that i saw that you executing it in a console project template. When i do this i get the same:

While i am not sure yet why this occurs, have you executed the examples like this all the time? if so, can you try creating a .fsx script file and send the code directly to F# interactive? If that works for you (This is how all of this was tested), we at least enclosed the error a bit.

I found the problem. The Http.fs version we used was encoding uri slashes with a hack using reflection and setting fields of objects. The accession of this field caused the NullReferenceException. I updated the package to use the Http.fs nuget package to handle http request creation and encoding. Streaming nodes and edges should work in program loops too.

It looks like this update also requires the latest version of Hopac to be installed. I ran into an error using just version 1.1.3
However, when I installed the latest version of Hopac (https://github.com/Hopac/Hopac) via NuGet, everything started working. So perhaps you could fix this by adding Hopac as a dependency as well (version 0.4.1 or higher)?

Yeah i just saw that, but this is a strange error as hopac is listed as dependency of Http.fs, not of the package itself. So i don't get why package management does not resolve this. I will check if adding hopac as dependency fixes the problem.

I can confirm that I was able to run both the examples after I installed hopac as a dependency.

I think i found the root of this problem:
paket (the package manager we use) uses a different strategy to resolve transitive dependencies then nuget. This also explains the problems you guys faced with the Newtonsoft.Json package dependency:
While paket resolves transient dependencies with the maximum version, nuget takes the minimum matching version. And this is how we end up with these dependency conflicts. I was not aware of this, sorry for all the confusion.
So what i will do now is emulate the nuget manager behaviour in our paket.dependencies file so that a package can be generated that is compatible with nuget manager out of the box.

That seems to have fixed the issue. I just tested v1.1.6 and both the examples seem to work :)

authors: PrashantVaidyanathan cgravill kMutagene

repo: CSBiology/FSharpGephiStreamer

license: mit

license_source: bigquery


text:
Support CUDA on Ubuntu18.04

This MR just adds an ubuntu 18.04 variable, and fixes the README to match.
I believe this simple fix should work, however I'm not sure how you would like this tested in order to confirm it.

Ubuntu 18.04 is now in the tests and it passes so I guess it is ok.

repo: CSCfi/ansible-role-cuda


text:
requirements中的torch版本冲突

你好，requirements中的torch版本冲突，torch=2.0 和pytorch=1.12.1，请问应该有那个版本的呢

使用pytorch=1.12.1，torch是peft的依赖库就顺便写了

可以不安装试一下，应该可以跑的

authors: CSHaitao zhangatao


text:
5.1.0 Record Format updates

Includes needed updates for 5.1.0 release, new cve-schema directory structure, and new names for schema files consistent with the record format naming.

@ccoffin sorry to jump into this old merged PR
Would you remember why you merged this CVSS v4 schema change from multipleOf to enum scores in https://github.com/CVEProject/cve-schema/pull/303/commits/84a2b1ed8bf98218a822843e06236c1e91cae0f8  ?
Was that a solution to avoid validation errors in python tooling?
see https://github.com/RedHatProductSecurity/cvelib/issues/87 for a related issue+solution (load json float as decimal instead of floats).

stop sending me these letters, someone made a mistake with my email, delete
the newsletter, I don’t need it
Ср, 3 июля 2024 г. в 16:28, Дмитрий Киселев @.***

:

Перестаньте мне присылать письма и удалите мой аккаунт, я не нуждаюсь в
этой рассылке …
Ср, 3 июля 2024 г. в 16:27, Loïc Jaquemet @.***>:

@ccoffin https://github.com/ccoffin sorry to jump into this old merged
PR
Would you remember why you merged this CVSS v4 schema change from
multipleOf to enum scores in 84a2b1e
https://github.com/CVEProject/cve-schema/commit/84a2b1ed8bf98218a822843e06236c1e91cae0f8
?
Was that a solution to avoid validation errors in python tooling?
see RedHatProductSecurity/cvelib#87
https://github.com/RedHatProductSecurity/cvelib/issues/87 for a
related issue+solution (load json float as decimal instead of floats).
—
Reply to this email directly, view it on GitHub
https://github.com/CVEProject/cve-schema/pull/303#issuecomment-2206076953,
or unsubscribe
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.
You are receiving this because you are subscribed to this thread.Message
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authors: Wildrussianman ccoffin trolldbois

repo: CVEProject/cve-schema


text:
not a bug just dumb I guess! Weathermap 98a to 1.3.1

I must be missing something, so let me say I am sorry to waste anyone's time. But I have been using Cacti and weathermaps
for quite a while, and I cannot see clear instructions on how to "upgrade" the weathermap plugin from 098a to v1.3.1. I have tested in non-prod, by disabling the plugin (DO NOT UNINSTALL), from the Linux console mv weathermap weathermap-old
copy the full repo (v1.3.1 dev) to weathermap folder and in the gui enable the new v1.3.1 weathermap. Obviously when I rename the 098a weathermap all of my current maps are in that folder structure. How to I convert them to this new version? Sorry to be a bonehead!

@edjchristopher, I'll have time to work on multiple issues after I wind down on Cacti 1.3 projects.  I hope you will have time to collaborate as I don't have a real good use case for the tool in my home office.

Sure I can help.
I was hopeful I could get weathermap v1.3.1 migration instructions as I cannot find any other than very old versions.

Just reach out when you are ready!!

@TheWitness Sure I can help.
I was hopeful I could just get weathermap v1.3.1 migration instructions as I cannot find any other than very old versions.

What time zone are you in?

Eastern time zone

Okay, perfect.

OK so. I have never had any problems with Cacti, yet I cannot get this plugin to work. I have replicated our Prod Cacti which was a repo install 1.2.27. Add in this weathermap plugin v1.3.1 it looks like it did ok. I cannot create a new map even. So I blew away that server and did a fresh install 1.2.27 (repo again) with weathermap v1.3.1 and get the same results. Looks ok but will not function, even creating a new map.
Is it possible it may be the repo install? Should I just get your download and do it all over again?
Thoughts?? I assume this is working somewhere?!?

Bring up your browsers debug page and see if you see any JavaScript errors.  Also check the Cacti log for errors.  When you upgrade, Cacti will attempt to move asset's to new folders, so you have to make sure that the apache has full access to the plugin directory.  If you pull the develop version, won't be able to install until you relocate the config.php.dist and move your output and config folders out of the plugin directory if you can manage it.

There could be bugs in that last bit.  Good thing it's not production.

authors: TheWitness edjchristopher


text:
seekr_graph with cross species classification

Hi Jessime,
I'm trying to use seekr_graph to find communities of lncRNAs within our transcriptome assembly of a non-model organism and compare it across species to GENCODE mouse ncRNAs.  I extracted the lncRNAs, normalized against the total StringTie assembly and repeated the process with GENCODE mouse to perform the pearson correlation.
Running the seekr_graph module consistently errors out though. seekr_graph with self vs self correlations functions perfectly but not using cross-species correlations.
Traceback (most recent call last):   File "/seekr/virtualenv/bin/seekr_graph", line 10, in <module>     sys.exit(console_graph())   File "/seekr/virtualenv/lib/python3.7/site-packages/seekr/console_scripts.py", line 500, in console_graph     float(args.resolution), int(args.n_comms), args.seed)   File "/seekr/virtualenv/lib/python3.7/site-packages/seekr/console_scripts.py", line 475, in _run_graph     maker.make_gml_csv_files()   File "/seekr/virtualenv/lib/python3.7/site-packages/seekr/graph.py", line 175, in make_gml_csv_files     self.build()   File "/seekr/virtualenv/lib/python3.7/site-packages/seekr/graph.py", line 166, in build     self.graph = networkx.from_pandas_adjacency(self.adj)   File "/seekr/virtualenv/lib/python3.7/site-packages/networkx/convert_matrix.py", line 185, in from_pandas_adjacency     raise nx.NetworkXError("Columns must match Indices.", msg % missing)
Thank you!

Hey, this is a great question. The answer is going to depend a on what experiment you're trying to perform, exactly.
seekr_graph expects a square adjacency matrix where the names of the rows match the names of the columns. Lets say that your species has n transcripts, and mouse has m transcripts. You would need to pass the whole, (n+m)^2 matrix, which would be asking the question, "What communities form if we throw all transcripts together and run community detection?"
Is this what you want to do? There isn't a neat tool to do it from the command line at this point, but I can write up something for you in Python.
Another approach would be to do the self vs. self communities for both, and then compare the communities afterwards, using something like normalized information. We've successfully used this approach in the past.

Hi Jessime,
We performed an RNA-Seq experiment for our non-model species and and are interested in the population of lncRNAs in our transcriptome assembly that are differentially expressed in two different conditions. I'd like to use seekr to identify non-coding genes that are in both our assembly and a well-annotated assembly like GENCODE human or mouse as a potential clue for their function in our organism.
I suppose the question being asked is, given a subset of lncRNAs that are DE: n(DE), which ones are similar to the total population of mouse lncRNAs, m. Is there an easy way to compare across species? I suppose it makes sense to perform self vs. self for both transcriptomes than compare between them. Would you recommend this strategy or something else entirely?
Thanks!

I still think there are several ways you could go about this. I'll show you how I would directly answer:

given a subset of lncRNAs that are DE: n(DE), which ones are similar to the total population of mouse lncRNAs, m?

as an example. Let's assume you've just finished running:
$ seekr_pearson DE_counts.csv mouse_counts.csv -o adj.csv

You could open python and run:
import pandas as pd

df = pd.read_csv('adj.csv', index_col=0)
mean_similarity = df.mean(axis=1).sort_values(ascending=False)
mean_similarity

This will give you a sorted list of how similar each DE transcript is to the mouse transcriptome, on average.
Alternatively, if the number of DE transcripts is fairly small (hundreds?) it might also make sense to see which DE transcripts fall into which mouse communities.

I don't think the communities are directly relevant to our work. We are more interested in identifying specifically conserved lncRNA in our assembly in relation to a well annotated species like mouse i.e. the likelihood that transcript n is Xist based on pearson correlation.  Does seekr support something like a one to one comparison between  two distinct lncRNAs? Would it be feasible to find the best cross-species pair that have the best pearson correlation or am I mistaken?

It sounds like all the information you want is just in adj.csv, right? It's just a matter of querying it to answer your question. Right now, the command line tools don't have a way to do this, but it's straightforward in python.
Using the example:

the likelihood that transcript n is Xist based on pearson correlation.

import pandas as pd

df = pd.read_csv('adj.csv', index_col=0)
most_xist_like = df['Xist-201'].sort_values(ascending=False)

Assuming you've labeled one of the mouse rows as Xist-201 (you can replace Xist-201 with the whole fasta header, another lncRNA, or whatever row you need), you'll have a sorted list of how similar each of your non-model transcripts are to Xist.

Hi Jessime!
Thanks for this. It was a great help. One thing I noticed was that there was a low degree of correlation between lncRNAs between species; even those that were evolutionarily conserved. This seems counterintuitive to me: wouldn't conserved lncRNAs have a high correlation due to having similar k-mer composition? Or am I just missing something?

Great, glad it's working out!
When you use 6mers, correlations are always pretty low, because of the large number of kmers in each profile. The math works out that as the length of two arrays approaches infinity, the correlation value between the arrays approaches 0, no matter the contents of the arrays. But even with the low values, we found that we could detect a significantly higher set of correlations between known homologs than other random comparisons.
I should say though that if your sole goal is to find evolutionary homologs, there are better tools than SEEKR, even for lncRNAs. SEEKR is probably better for detecting functional similarity.

hello.
I have a similar question. I want to find cross-species homologs of lncRNA and protein-coding genes. I just put all of them in a same fasta file. Can it work?
It seem like in your manuscript, humans and mouse are separately run seekr_kmer_counts. Then using seekr_compare compare them similarity.
which one is more suitable?  Or they are the different routes to the same goal?

Hey @huanananan,
The difference between putting the species in the same file versus different files isn't going to be huge, but it might be significant. The difference between the two is the baseline normalization will change. If you have the time, I'd recommend trying both and seeing which works better for you.
If you only want to use one approach, I'd suggest keeping the files separate. This does two things:

The normalization for each species is then relative only to itself, which I think makes more sense.
The output file size is going to be much smaller this way.

Thank you. Very helpful.

Of course. I'm going to go ahead and close this issue since it's pretty old. But feel free to open new ones if you run into other questions/issues with seekr!

authors: Jessime huanananan kmothera

repo: CalabreseLab/seekr


text:
希望能设置多个额度提醒阈值

例行检查

[x] 我已确认目前没有类似 issue
[x] 我已确认我已升级到最新版本
[x] 我已完整查看过项目 README，已确定现有版本无法满足需求
[x] 我理解并愿意跟进此 issue，协助测试和提供反馈
[x] 我理解并认可上述内容，并理解项目维护者精力有限，不遵循规则的 issue 可能会被无视或直接关闭

功能描述
希望能设置多个额度提醒阈值
应用场景
有的人用的快有的人用的慢，需要的提醒阈值不同

ps: 部分二开允许用户自己设置提醒阈值，也可以考虑借鉴一下

repo: Calcium-Ion/new-api


text:
ludo: Add version 0.16.20

Closes #297

[x] I have read the Contributing Guide.

/verify

/verify

/verify

repo: Calinou/scoop-games


text:
plot_period_transactions gives different graphs with the same model

I've noticed that when I use the plot_period_transactions() function several times in a row (with the same trained model), I get slightly different graphs on the model frequency transactions.
More concretely the following code will show 3 different graphs:
from lifetimes.datasets import load_cdnow_summary

data = load_cdnow_summary(index_col=[0])

bgf = BetaGeoFitter(penalizer_coef=0.0)
bgf.fit(data['frequency'], data['recency'], data['T'])

plot_period_transactions(bgf)
plot_period_transactions(bgf)
plot_period_transactions(bgf)

Can anyone explain the reason for such a behaviour?

There's a random data generation process in the background

I've noticed that when I use the plot_period_transactions() function several times in a row (with the same trained model), I get slightly different graphs on the model frequency transactions.

How much data do you have? I would expect the variations to smooth out once you have a big enough database...
It would be a curious and useful feature to have some sort of way of calculating the variance on the predictions given by the model itself though.

Subsequent calls of the  plot_period_transactions routine yields slightly different results due to simulation implementation which is based on random number generator. I checked it up in the source code. It's fine.
But why did'n you applied the analytical results from “Counting Your Customers” the Easy Way:
An Alternative to the Pareto/NBD Model?

Using formula (8) and taking into account the (age of each individual customer, you always get the exact result, no matter how many times you invoke the routine.
Or am I missing a hidden point in using the simulation instead of analytical approach? Maybe performance? (Eq. (8) is not trivial to calculate.)  Thank you guys.

authors: CamDavidsonPilon psygo rando128 zbazanowski

repo: CamDavidsonPilon/lifetimes


text:
iOS輸入法介紹度可以加埋系統內置嘅粵拼輸入法

iOS 16同macOS Ventura都已經支援粵拼輸入，我而家用咗幾個月覺得幾好用。可唔可以加埋到個guide度？

@xyu38 而家重寫緊個網站

authors: AlienKevin laubonghaudoi


text:
Add --remove-uncalled-funcs

Fixes most of #85. Not enabled by default but is a relatively safe optimization. It might break some indirects? (if they don't use funcRef somehow)
Example:
$ ./porf -e "console.log(1)" -b --no-run
wasm size: 39234 bytes
$ ./porf -e "console.log(1)" -b --no-run --remove-uncalled-funcs
wasm size: 27428 bytes
$ ./porf -e "console.log(1)" -b --no-run --remove-uncalled-funcs --uncalled-funcs-runs=5
wasm size: 22441 bytes

Some other examples for comparision:
$ ./porf -e "Porffor.miniLog(1)" -b --no-run
wasm size: 23326 bytes
$ ./porf -e "Porffor.miniLog(1)" -b --no-run --remove-uncalled-funcs
wasm size: 15604 bytes
$ ./porf -e "Porffor.miniLog(1)" -b --no-run --remove-uncalled-funcs --uncalled-funcs-runs=5
wasm size: 11970 bytes
$ # and our obvious winner:
$ ./porf -e "Porffor.numberLog(1)" -b --no-run
wasm size: 115 bytes

A 30% wasm size reduction for console.log :tada: (and potentially up to 42% :eyes:)

I don't think this is needed anymore with latest rewrites?

I agree yes, I'll close it now.

authors: BobVarioa CanadaHonk

repo: CanadaHonk/porffor


text:
pytorch and cuda version

hello,
what's the version of your pytorch and cuda? I tried many versions but all failed.

Hello Han,
The code should work with most versions of Cuda. Most of the code was developed and trained in Cuda 9, but I have also gotten it running on Cuda 10.0 and Cuda 10.2 (tested today).
I think the trickier part is to align Pytorch and Transformers:
In the requirements.txt I recommend transformers==3.1.0.
I don't recommend a particular version of torch, as I think it will automatically pick one that's compatible, but for reference, I am using torch==1.7.0 (with Cuda 10.2) and it is working out of the box.
Choosing the right torch version is a bit tricky and depends on the Cuda you have installed (as well as OS). I usually use this page: https://pytorch.org/get-started/previous-versions/ to decide which Torch version to install, it is kept up to date.
Hope this helps, if you share the error message you're getting I can try to help more!
And sorry for the delay!
Philippe


text:
dasymeter, expatiation

This pull request was generated by the 'mq' tool

/trunk merge

repo: Canva/mergequeue-trunk


text:
test-pr-42-c268aced-274b-4637-8d45-376877ac7e48

test pull request for owner check

/trunk merge


text:
设置为循环播放后，不会执行onAutoCompletion方法吗？

问题描述：
设置为循环播放后，播放完成，不会执行onAutoCompletion方法吗？
如果有其他的回调方法，是哪个呢

同问

同问，

……肯定不会执行啊，执行了就释放了。。。
循环播放就像是动画的repeat -1一样，你如果需要的话，可以外部监听进度实现循环播放的次数监听

authors: CarGuo barryyanggoing kyriej weifengteng

repo: CarGuo/GSYVideoPlayer


text:
请问大神，如何与Rxffmpeg配合使用？

问题描述：
如何与Rxffmpeg配合使用？我的项目本身已经集成Rxffmpeg,但是看到GSYVideoPlayer集成时候还有ffmpeg的so，这样重复会不会导致兼容性或者包过大。
GSY依赖版本
例如 implementation 'com.shuyu:gsyVideoPlayer-java:7.0.1'

Rxffmpeg的so是经过精简的，去掉了不常用的编解码器，所以想使用Rxffmpeg的so，能减少包的大小，不知道GSYVideoPlayer如何与Rxffmpeg集成使用？

这个还真不兼容这样的方式·····


text:
Change appbar to sidepanel

Nice change, thanks!

authors: Carael glucaci

repo: Carael/CrossBusExplorer


text:
🛑 jereconstructionroofing is down

In b2e4764, jereconstructionroofing (jereconstructionroofing.com) was down:

HTTP code: 429
Response time: 426 ms

Resolved: jereconstructionroofing is back up in 5e0d606 after 3 hours, 25 minutes.

repo: Careas/vps-monitor


text:
I'm getting "+" as the start sentinal for Track 3

Track 3 wasn't showing up on the demo until I messed with the regexp to accept a plus for that track:
var pattern = new RegExp("^(%[^%;\\?]+\\?)(;[0-9\\:<>\\=]+\\?)?([+;][0-9\\:<>\\=]+\\?)?","i");
I have two slightly different models of card reader and both of these output "+" to denote the start of track 3 data. Other than that minor detail, this plugin is exactly what I needed. Thanks.

Also, can I offer the following suggestion so the default parser will trim off the sentinel characters (in the cardData)...
line1: match[1] ? match[1].substr(1, match[1].length-2) : ""

Thanks. These are good suggestions, and I'll incorporate them.
What kind of card are you scanning? I don't have any 3-track cards, so I'm not surprised to hear there's a bug.

These are just standard 3 track HiCo magstripe cards, we print them ourselves for several different applications. Track 3 was not in use, but I've started adding a variable length ID number for another application.

Fix incorporated in "events" branch.

authors: CarlRaymond Sam-Hall


text:
ValueError: setting an array element with a sequence.

An input of one filename as a singleton list works, but a list of two filenames raises an error.
Good input:
ADTBDRNN(['simple_loop.wav'])

Output:
[array([ 0.        ,  0.04643991,  0.52244898,  0.52244898,  0.98684807,
         0.99845805,  1.04489796,  1.24226757,  1.24226757,  1.30031746,
         1.52090703,  1.52090703,  1.59056689]),
 array(['BD', 'HH', 'SD', 'HH', 'BD', 'HH', 'BD', 'BD', 'HH', 'BD', 'SD',
        'HH', 'HH'],
       dtype='|S32')]

Good input:
ADTBDRNN(['125_bounce.wav'])

Output:
[array([ 0.49922902,  0.510839  ,  0.58049887,  0.95201814,  0.95201814,
         1.45124717,  1.53251701,  2.31038549,  2.41487528,  2.47292517,
         2.80961451,  3.36689342,  3.44816327,  3.81968254,  3.81968254,
         4.23764172,  4.34213152,  4.42340136,  5.09678005,  5.29414966,
         5.36380952,  6.33904762,  6.6060771 ,  7.0124263 ,  7.05886621,
         7.20979592,  7.27945578,  7.43038549]),
 array(['SD', 'HH', 'HH', 'HH', 'BD', 'SD', 'HH', 'BD', 'SD', 'HH', 'BD',
        'SD', 'HH', 'HH', 'SD', 'BD', 'SD', 'HH', 'BD', 'SD', 'HH', 'HH',
        'BD', 'BD', 'SD', 'SD', 'SD', 'HH'],
       dtype='|S32')]

Bad Input:
ADTBDRNN(['simple_loop.wav', '125_bounce.wav'])

Output:
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-8-88f3a1bbf5de> in <module>()
----> 1 ADTBDRNN(['simple_loop.wav', '125_bounce.wav'])

/Library/Python/2.7/site-packages/ADTLib/models/__init__.pyc in ADTBDRNN(TrackNames, out_sort, ret, out_text, savedir, close_error, lambd)
     85             P[j][i]=peak
     86
---> 87     P=arrange_output(P,output_sort=out_sort)
     88
     89     if out_text == 'yes':

/Library/Python/2.7/site-packages/ADTLib/utils/__init__.pyc in arrange_output(Inputs, output_sort)
     40
     41         Out[i]=list(np.zeros(len(Inputs[i])))
---> 42         Out1[i]=list(np.zeros((1,2)))
     43         for j in xrange(len(Inputs[i])):
     44             Out[i][j]=list(np.zeros((len(Inputs[i][j]))))

ValueError: setting an array element with a sequence.

Hi Steve
Thanks for brining this to my attention, an error was made in the previous update, this should now work.
All the best,
Carl

authors: CarlSouthall stevetjoa

repo: CarlSouthall/ADTLib


text:
SIMD approach for parsing of 8 UTF-16 digits should be as efficient as possible

We should make sure that the code we use is at least as efficient as the routine in this StackOverflow answer:
public unsafe uint ParseUint(string text)
{
    fixed (char* c = text)
    {
        Vector128<byte> mul1 = Vector128.Create(0x14C814C8, 0x010A0A64, 0, 0).AsByte();
        Vector128<short> mul2 = Vector128.Create(0x00FA61A8, 0x0001000A, 0, 0).AsInt16();
        Vector128<long> shift_amount = Sse2.ConvertScalarToVector128Int32(8 - text.Length << 3).AsInt64();

        Vector128<short> vs = Sse2.LoadVector128((short*)c);
        Vector128<byte> vb = Sse2.PackUnsignedSaturate(vs, vs);
        vb = Sse2.SubtractSaturate(vb, Vector128.Create((byte)'0'));
        vb = Sse2.ShiftLeftLogical(vb.AsInt64(), shift_amount).AsByte();

        Vector128<int> v = Sse2.MultiplyAddAdjacent(Ssse3.MultiplyAddAdjacent(mul1, vb.AsSByte()), mul2);
        v = Sse2.Add(Sse2.Add(v, v), Sse2.Shuffle(v, 1));
        return (uint)v.GetElement(0);
    }
}

The c - '0' operation could be part of the range check.
The add(v,v) can be put into the multiplier, when using int16 instead of int8.
	// Pure SSE2.
	// A naive port to NEON should be straight forward (just re-work the conditional).
	__m128i v = _mm_loadu_si128((__m128i*)(void*)src);
	v = _mm_add_epi16(v, _mm_set1_epi16(0x7FC6));
	v = _mm_subs_epi16(v, _mm_set1_epi16(0x7FF6));
	if (_mm_movemask_epi8(v) == 0) { /* has eight UTF-16 LE digits */
		v = _mm_madd_epi16(v, _mm_set_epi16(1, 10, 100, 1000, 1, 10, 100, 1000));
		v = _mm_packs_epi32(v, v);
		v = _mm_madd_epi16(v, _mm_set_epi16(0, 0, 0, 0, 1, 1, 10000, 10000));
		v = _mm_add_epi32(v, _mm_shuffle_epi32(v, 1));
		return (unsigned)_mm_cvtsi128_si32(v);
	}

I'd like credit if y'all use the "shift off the bad chars method".
but otherwise I don't need (or want) credit for something this simple.
I wonder if using pmuludq would allow the multiplies to run in parallel...

Been trying to benchmark the two approches  (eval1 & eval2)
simplified version in which range check is omited
eval1 :
  Vector128<short> raw = Sse41.LoadDquVector128((short*)start);
  Vector128<short> mask0 = Vector128.Create((short)48); // adapter à la longueur
  raw = Sse41.SubtractSaturate(raw, mask0);
  Vector128<short> mul0 = Vector128.Create(10, 1, 10, 1, 10, 1, 10, 1);
  Vector128<int> res = Sse41.MultiplyAddAdjacent(raw.AsInt16(), mul0);
  Vector128<int> mul1 = Vector128.Create(1000000, 10000, 100, 1);
  res = Sse41.MultiplyLow(res, mul1);
  Vector128<int> shuf = Sse41.Shuffle(res, 0x1b); // 0 1 2 3 => 3 2 1 0
  res = Sse41.Add(shuf, res);
  shuf = Sse41.Shuffle(res, 0x41); // 0 1 2 3 => 1 0 3 2
  res = Sse41.Add(shuf, res);
  value = (uint)res.GetElement(0);

eval2 :
  Vector128<short> raw = Sse41.LoadDquVector128((short*)start);
  Vector128<byte> mul1 = Vector128.Create(0x14C814C8, 0x010A0A64, 0, 0).AsByte();
  Vector128<short> mul2 = Vector128.Create(0x00FA61A8, 0x0001000A, 0, 0).AsInt16();
  Vector128<byte> vb = Sse2.PackUnsignedSaturate(raw, raw);
  vb = Sse2.SubtractSaturate(vb, Vector128.Create((byte)'0'));
  Vector128<int> v = Sse2.MultiplyAddAdjacent(Ssse3.MultiplyAddAdjacent(mul1, vb.AsSByte()), mul2);
  v = Sse2.Add(Sse2.Add(v, v), Sse2.Shuffle(v, 1));
  value = (uint)v.GetElement(0);

here's the result I obtain for 850 000 random 8 digit numbers

Method
Mean
Error
StdDev
Median
Ratio
RatioSD

EvalParse_1
6.381 ms
0.1258 ms
0.2625 ms
6.394 ms
1.00
0.00

EvalParse_2
6.338 ms
0.1518 ms
0.4331 ms
6.181 ms
1.02
0.08

Looks like pretty close performance for both.

It is a micro-optimization.  The difference between EvalParse_1 and EvalParse_2 is 5 cycles of latency and 1 uop.
A EvalParse_2 without the add(v,v) saves an additional 1 uop, but has the same latency.  The split multiply version saves ~3 cycles of latency at the cost of ~3 uops.
An improved range check saves 1 cycle of latency and 1 uop.

authors: CarlVerret aqrit lemire

repo: CarlVerret/csFastFloat


text:
List function

Would be good to have a list function for the bot to check who has the next birthday

Added in #4.

repo: Carnagion/birthbot


text:
Fix wrong bound selection in histogram last bucket

Fixes:
https://github.com/CartoDB/support/issues/1871
Useful comments found in an older closed issue:
https://github.com/CartoDB/carto.js/issues/926

Let me know if you want me to check in Builder and give you the acceptance.

Let's see first is @VictorVelarde can have a look and make a CR and then yes, it will be very helpful if you could test it in Builder!

The fix LGTM @csubira, and it seems like there is no 'one duplicated bucket issue', so I think we can move on. I have just added 2 specs and made a little refactor to an if, and that's it.
Feel free to merge it

@csobier @VictorVelarde next time ask me for checking the change on staging!

I will Ramiro. Indeed I'll ask you for acceptance after merging another carto.js PR and releasing a new version

authors: VictorVelarde csubira ramiroaznar


text:
Fixes tiler request when the vizjson contains a named map and a torque layer with a named map

We check if the vizjson contains a named map and torque layer with a named map and in that case, we don't send the torque layer in the request.

retest this please

@CartoDB/frontend / @javisantana: can you please have a look at this PR, please?

I'd add a test, this is an edge case that cen be missed in the future pretty easily

@javisantana: spec added. The code was fine for you?

yes yes :es:

Thanks!

authors: javierarce javisantana


text:
Auth API UI

Goal: Implement the proposed UI for the new Auth API.
Links:

Auth API project
Invision project
Auth API reference

Auth API Keys pages must provide the UI to the new Auth API
Top levels operations are:

Regenerating the master key.
Edit the public key settings.
Create, regenerate and delete regular keys.

As you can check in the attached Invision project, there are two main forms:

API keys list. First key is the master key, the second one is the public key and then the regular ones.
API key settings page: this form has two differents ways of presenting the information:

For the public key: you can change APIs access and dataset Read access. Notice that there's only read access for this kind of key.
For the regular ones: you can set APIs access and CRUD operations for each dataset. These keys can't be edited.

NOTES:

There's neither Import nor Analysis API even though they're present in the mockup.
The link icon copies the key to the clipboard.
Now this page must get all the user datasets. It's not clear what happens with shared datasets so far so let's begin getting only your own datasets.

Hi!
Right now there is also a section related to Google API keys, what are we doing with it? Are we still showing it under the same conditions? Are we removing it?

Hi again! I'm adding the regenerate and delete buttons functionality, and it seems a little bit weird to remove the key or regenerate it without a previous warning to the user, do you think we should add a dialog/modal alerting the user before regenerating/deleting the key?
cc @CartoDB/design

AFAIK that action can be extremely destructive, so I would definitely warn the user about the consequences.
Regarding the Google API Keys... no idea. Surely someone else can give you a better answer than us. I'm not sure who, though. Sorry!

Good catch, Ruben.
@inigomedina What do we do with the Google Maps form? We have two options:

Keep it below the keys section as it is right now. That will move it down and perhaps it's a bit hard to find but it's my preferred option.
Create a tab only for Google Maps: easier to find, harder to develop as it will require changes both in API keys and Mobile apps page.

Design-wise, I would go with the first option. Makes more sense having all your keys grouped in the same place than separated into tabs. But then I would probably rename the tab from "CARTO" to Keys, API Keys or something like that.

Design-wise, I would go with the first option. Makes more sense having all your keys grouped in the same place than separated into tabs. But then I would probably rename the tab from "CARTO" to Keys, API Keys or something like that.

Yes, we go with the first option. Good enough for this step.
If we face issues regarding the visibility of those external keys, we can always include anchor links from an introduction content to the different parts of the page. But right now we don't need that.
Just replicate the same structure of the page we had in Editor and let's see.

I've added some placeholders to show when the user has no datasets, or when the search result is empty, what do you think @piensaenpixel?

I had a conversation this morning with @javitonino  regarding the public and master API keys:
We decided to show in public API show view the list of public datasets, and in the regular keys form view we were going to select by default, and disabled, the read checkbox for public datasets, but not sending that information to the backend, this lead to that permission not being returned in the GET request of the API keys, which lead to inconsistencies between the UI and the API.
After some more thought and another conversation with @inigomedina, we decided to change that behavior, we won't select anything by default in the form view, the user will have to select them explicitly.

We need to address changes also in organization tabs. This will be made outside the current migration to deliver sooner.
More info in this ticket https://github.com/CartoDB/cartodb/issues/13559

The Auth API UI has been deployed to https://apikeys.carto-staging.com/your_apps.
Username: apikeys
Password: apikeys123

While doing a small acceptance I realized that the title could be improved, right now we're showing:

which could make sense when you are creating a new API key, since you have to configure it first, but when the API key is already created you can't configure/edit it, so I think we could change the title to something like Your API key details, what do you think @piensaenpixel?

If there is no action, we shouldn't use any verb. Your solution, in that case, looks good.
However, if there is some kind of action, but not one so specific like edit or configure, we could just go for a generic one like Manage your API key.

Maps API only understands select grants, but the UI allows you to choose others as well. After discussing on the Auth API slack channel, we're going to leave it as it is at least for now. Otherwise, looks good to me.

+1 to @inigomedina comments

Did a quick pass, found some issue:

Datasets with privacy == link do not show up in the default public key listing (and they should).
Styles look weird, at least in firefox (spacing btween previous input and next header):

Master/default_public keys do not show the [MAPS] [SQL] tags (and they have them). On purpose?
Create a new api key, mark an insert permission, mark the Maps API, save. The API key has that insert permission but is not displayed in the UI
Only the first 20 api keys are shown. The api_keys endpoint has paging (default per_page = 20) but it seems frontend does not implement it.

Pending:

Test with organizations

So, in the public key we should show the shared datasets, right?
I'll take care of that, also check IE and Safari
Master and default_public don't show any API tags
That was a last-hour change, we decided to hide some checkbox when only maps API is selected which solves some problems but leave us with that corner case, anyway, that permission won't work.
We didn't take into account the pagination, neither in design or in code, we should talk about this

I was speaking about datasets with privacy set to LINK. About shared datasets, the public api key will have access to shared datasets that are public/link. However, maybe we should not show that, as we decided not to support organization shares in api keys for now, so it would be consistent to not show shared datasets here as well)
:+1:
Ok, just felt strange in comparison with the others
Ok, it is weird, but I guess it's enough of an edge case to ignore.
:dancer: We have per_page and page query parameters to do this. An alternative would be to impose a limit to the number of api keys per user.

We should probably remove this: Learn more about using your simple API key in CARTO from the bottom of the page. Maybe replace it for a link to the new docs. For sure, remove that simple now that our api keys rock :D

Yes, @javitonino. We should replace that link for a new one bringing users to the new docs, specifically to the fundamentals section regarding authorization. We didn't include it on the roadmap of Auth since it wasn't clear that the developer center would be available at the time of its launch. Let me think about the final URL, and when we have something ready to be implemented, I'll just create a PR.

authors: arianaescobar danicarrion inigomedina ivanmalagon javitonino jesusbotella piensaenpixel rubenmoya

repo: CartoDB/cartodb


text:
create feature flag for data-library

for this to work only with selected users (starting with common-data)

Created data_library feature flag and activated in common-data user

authors: ethervoid matallo


text:
[Auto-generated] Update dependencies

Update dependencies
Automatically created PR from ci/dependabot-updates.
The PR is based on the 'CI - Update dependencies PR' workflow in SINTEF/ci-cd.
To do

[ ] Check that the diff is sensible, and that tests and builds pass with the new dependency versions.

Stay at pydantic v1

repo: CasperWA/voila-optimade-client


text:
Action - Intersect Discord Channel Setup

[x] Setup Swarm Project Management channel
[x] Setup Intersect Town Hall channel - to be created in Town Square section
[ ] Resolve event calendar access

Channel Created
https://discord.com/channels/1136727663583698984/1245340231482474506

We have the all the access and everything is set up , but chronicle bot breaks to include in Discord Events.

authors: stephen-rowan whitevo

repo: Catalyst-Swarm/Intersect-Town-Hall