Merge branch 'develop' into SYNPY-1304-otel-in-synpy

Sage-Bionetworks · Nov 3, 2023 · 803ebe4 · 803ebe4
2 parents 3a24d64 + 0c199dd
commit 803ebe4
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -26,8 +26,19 @@ on:
 
 jobs:
 
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - uses: pre-commit/[email protected]
+
+
   # run unit (and integration tests if account secrets available) on our build matrix
   test:
+    needs: [pre-commit]
 
     strategy:
       matrix:
@@ -39,7 +50,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
@@ -65,7 +76,7 @@ jobs:
             ${{ steps.get-dependencies.outputs.site_bin_dir }}
           key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v7-otel
 
-      - name: install-py-dependencies
+      - name: Install py-dependencies
         if: steps.cache-dependencies.outputs.cache-hit != 'true'
         shell: bash
         run: |
@@ -80,11 +91,6 @@ jobs:
             pip install numpy
           fi
 
-      # - name: lint
-      #   shell: bash
-      #   run: |
-      #     flake8
-
       - name: run-unit-tests
         shell: bash
         run: |
@@ -138,15 +144,9 @@ jobs:
             pytest -sv tests/integration/synapseclient/test_command_line_client.py
           fi
 
-  # enforce the code matches the Black code style
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: psf/black@stable
   # on a GitHub release, build the pip package and upload it as a GitHub release asset
   package:
-    needs: [test,lint]
+    needs: [test,pre-commit]
 
     runs-on: ubuntu-20.04
 
@@ -157,7 +157,7 @@ jobs:
       bdist-package-name: ${{ steps.build-package.outputs.bdist-package-name }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,4 +1,5 @@
-exclude: '^docs/conf.py'
+exclude: '^docs/conf.py|^docs/build/'
+
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks

diff --git a/Pipfile.lock b/Pipfile.lock
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e61f33e16f39e8cbda346a2c639c4799
+config: 90d422e4b09fda20663a5d255dc16438
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.1.0',
+    VERSION: '3.1.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/build/html/api/Activity.html b/docs/build/html/api/Activity.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Provenance &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Provenance &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -247,7 +247,7 @@ <h2>Activity<a class="headerlink" href="#activity" title="Permalink to this head
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -268,7 +268,7 @@ <h2>Activity<a class="headerlink" href="#activity" title="Permalink to this head
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">

diff --git a/docs/build/html/api/Annotations.html b/docs/build/html/api/Annotations.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Annotations &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Annotations &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -199,7 +199,7 @@ <h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headli
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -220,7 +220,7 @@ <h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headli
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">

diff --git a/docs/build/html/api/Client.html b/docs/build/html/api/Client.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Client &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Client &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -1643,7 +1643,7 @@ <h2>More information<a class="headerlink" href="#more-information" title="Permal
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -1664,7 +1664,7 @@ <h2>More information<a class="headerlink" href="#more-information" title="Permal
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">

diff --git a/docs/build/html/api/Entity.html b/docs/build/html/api/Entity.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Entity &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Entity &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -461,7 +461,7 @@ <h2>Properties and annotations, implementation details<a class="headerlink" href
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -482,7 +482,7 @@ <h2>Properties and annotations, implementation details<a class="headerlink" href
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">

diff --git a/docs/build/html/api/Evaluation.html b/docs/build/html/api/Evaluation.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Evaluations &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Evaluations &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -277,7 +277,7 @@ <h2>Submission Status<a class="headerlink" href="#submission-status" title="Perm
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -298,7 +298,7 @@ <h2>Submission Status<a class="headerlink" href="#submission-status" title="Perm
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">