Merge branch 'develop' into SYNPY-1064-speed_up_integration_tests

Sage-Bionetworks · Apr 19, 2021 · e05e7e5 · e05e7e5
2 parents dac6de8 + 6c5c431
commit e05e7e5
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -150,6 +150,10 @@ jobs:
 
     if: github.event_name == 'release'
 
+    outputs:
+      sdist-package-name: ${{ steps.build-package.outputs.sdist-package-name }}
+      bdist-package-name: ${{ steps.build-package.outputs.bdist-package-name }}
+
     steps:
       - uses: actions/checkout@v2
 
@@ -197,33 +201,61 @@ jobs:
         run: |
           python3 -m pip install --upgrade pip
           python3 -m pip install setuptools
+          python3 -m pip install wheel
 
           # install synapseclient
           python3 setup.py install
 
           # create distribution
-          python3 setup.py sdist
+          python3 setup.py sdist bdist_wheel
+
+          SDIST_PACKAGE_NAME="synapseclient-${{env.VERSION}}.tar.gz"
+          BDIST_PACKAGE_NAME="synapseclient-${{env.VERSION}}-py3-none-any.whl"
+          RELEASE_URL_PREFIX="https://uploads.github.com/repos/${{ github.event.repository.full_name }}/releases/${{ github.event.release.id }}/assets?name="
+
+          echo "::set-output name=sdist-package-name::$SDIST_PACKAGE_NAME"
+          echo "::set-output name=bdist-package-name::$BDIST_PACKAGE_NAME"
 
-          echo "PACKAGE_NAME=synapseclient-${{env.VERSION}}.tar.gz" >> $GITHUB_ENV
+          echo "::set-output name=sdist-release-url::${RELEASE_URL_PREFIX}${SDIST_PACKAGE_NAME}"
+          echo "::set-output name=bdist-release-url::${RELEASE_URL_PREFIX}${BDIST_PACKAGE_NAME}"
 
-      # upload the artifact to the GitHub Action
-      - name: upload-build-artifact
+      # upload the packages as build artifacts of the GitHub Action
+
+      - name: upload-build-sdist
         uses: actions/upload-artifact@v2
         with:
-          name: synapseclient
-          path: dist/${{ env.PACKAGE_NAME }}
+          name: ${{ steps.build-package.outputs.sdist-package-name }}
+          path: dist/${{ steps.build-package.outputs.sdist-package-name }}
 
-      # upload the artifact as an asset of the GitHub Release
-      - name: upload-release-asset
+      - name: upload-build-bdist
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ steps.build-package.outputs.bdist-package-name }}
+          path: dist/${{ steps.build-package.outputs.bdist-package-name }}
+
+      # upload the packages as artifacts of the GitHub release
+
+      - name: upload-release-sdist
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          upload_url: https://uploads.github.com/repos/${{ github.event.repository.full_name }}/releases/${{ github.event.release.id }}/assets?name=${{ env.PACKAGE_NAME }}
-          asset_name: ${{ env.PACKAGE_NAME }}
-          asset_path: dist/${{ env.PACKAGE_NAME }}
+          upload_url: ${{ steps.build-package.outputs.sdist-release-url }}
+          asset_name: ${{ steps.build-package.outputs.sdist-package-name }}
+          asset_path: dist/${{ steps.build-package.outputs.sdist-package-name }}
           asset_content_type: application/gzip
 
+      - name: upload-release-bdist
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.build-package.outputs.bdist-release-url }}
+          asset_name: ${{ steps.build-package.outputs.bdist-package-name }}
+          asset_path: dist/${{ steps.build-package.outputs.bdist-package-name }}
+          asset_content_type: application/zip
+
+
   # re-download the built package to the appropriate pypi server.
   # we upload prereleases to test.pypi.org and releases to pypi.org.
   deploy:
@@ -237,9 +269,16 @@ jobs:
         with:
           python-version: 3.6
 
-      - uses: actions/download-artifact@v2
+      - name: download-sdist
+        uses: actions/download-artifact@v2
+        with:
+          name: ${{ needs.package.outputs.sdist-package-name }}
+          path: dist
+
+      - name: download-bdist
+        uses: actions/download-artifact@v2
         with:
-          name: synapseclient
+          name: ${{ needs.package.outputs.bdist-package-name }}
           path: dist
 
       - name: deploy-to-pypi

diff --git a/docs/Credentials.rst b/docs/Credentials.rst
@@ -6,7 +6,7 @@ There are multiple ways one can login to Synapse. We recommend users to choose t
 
 One Time Login
 ==============
-Use `username` and `password` to login as follows::
+Use :code:`username` and :code:`password` to login as follows::
 
     import synapseclient
     syn = synapseclient.login("username", "password")
@@ -17,7 +17,53 @@ Alternately you can login using a personal access token obtained from synapse.or
 
     syn = synapseclient.login(authToken="authtoken")
 
-Use `.synapseConfig`
+Use Environment Variable
+=========================
+
+Setting the :code:`SYNAPSE_AUTH_TOKEN` environment variable will allow you to login
+to Synapse with a personal access token.
+
+The environment variable will take priority over credentials in the user's :code:`.synapseConfig` file
+or any credentials saved in a prior login using :code:`syn.login(rememberMe=True)`.
+
+.. TODO: Once documentation for it is written, link to documentation about generating a personal access token
+
+In your shell, you can pass an environment variable to Python inline by defining it before the command:
+
+.. code-block:: bash
+
+    SYNAPSE_AUTH_TOKEN='<my_personal_access_token>' python3
+
+Alternatively you may export it first, then start: Python
+
+.. code-block:: bash
+
+    export SYNAPSE_AUTH_TOKEN='<my_personal_access_token>'
+    python3
+Once you are inside Python, you may simply login without passing any arguments:
+
+.. code-block:: python3
+
+    import synapseclient
+    syn = synapseclient.login()
+
+To use the environment variable with the command line client, simply substitute :code:`python` for the :code:`synapse` command
+
+.. code-block:: bash
+
+    SYNAPSE_AUTH_TOKEN='<my_personal_access_token>' synapse get syn123
+    SYNAPSE_AUTH_TOKEN='<my_personal_access_token>' synapse store --parentid syn123 ~/foobar.txt
+
+Or alternatively, for multiple commands:
+
+.. code-block:: bash
+
+    export SYNAPSE_AUTH_TOKEN='<my_personal_access_token>'
+    synapse get syn123
+    synapse store --parentid syn123 ~/foobar.txt
+
+
+Use :code:`.synapseConfig`
 ====================
 For writing code using the Synapse Python client that is easy to share with others, please do not include your credentials in the code. Instead, please use `.synapseConfig` file to manage your credentials.
 
@@ -28,20 +74,20 @@ When installing the Synapse Python client, the `.synapseConfig` is added to your
     #password = <password>
     #authtoken = <authtoken>
 
-To enable this section, uncomment it. You will only need to specify either a `username` and `password` pair, or an `authtoken`. For security purposes, we recommend that you use `authtoken` instead of your `password`. A personal access token generated from your synapse.org Settings can be used as your *.synapseConfig* authtoken.
+To enable this section, uncomment it. You will only need to specify either :code:`username` and :code:`password` as a pair, or :code:`authtoken`. For security purposes, we recommend that you use :code:`authtoken` instead of :code:`username` and :code:`password`. A personal access token generated from your synapse.org Settings can be used as your *.synapseConfig* authtoken.
 
 ::
 
     [authentication]
     authtoken = <authtoken>
 
-Now, you can login without specifying your `username` and `password`::
+Now, you can login without specifying any arguments::
 
     import synapseclient
     syn = synapseclient.login()
 
-The .synapseConfig also supports a legacy `apikey` which can be used with a `username` instead of the `password` or `authtoken`, however api key support in the synapseConfig is considered deprecated in favor of personal access tokens which
-can be scoped to certain functions and which are revocable. If needed your legacy `apikey` can also be obtained from your synapse.org Settings.
+For legacy compatibility, the :code:`.synapseConfig` :code:`[authentication]` section also supports :code:`apikey`, which can be used instead of :code:`username` + :code:`password` pair, or :code:`authtoken`, however :code:`apikey` support in the .synapseConfig is considered deprecated in favor of personal access tokens (:code:`authtoken`) which
+can be scoped to certain functions and are revocable. If needed, your legacy :code:`apikey` can also be obtained from your synapse.org Settings.
 
 Letting the Operating System Manage Your Synapse Credentials
 ============================================================
@@ -51,9 +97,10 @@ For users who would like to save their credentials and let other OS configured a
     import synapseclient
     syn = synapseclient.login("username", "password", rememberMe=True)
 
-The application (keychain in Mac) will then prompt you to allow Python to access these credentials. Please choose “Yes” or “OK”.
+The application (keychain in Mac) will then prompt you to allow Python to access these credentials. Please choose "Yes" or "OK".
 
-The second time you login, you will not have to enter your `username` or `password`::
+The second time you login, you will not have to enter any arguments to :code:`login()`::
 
     import synapseclient
     syn = synapseclient.login()
+
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: 28b32c8cad55c715a9d6bb541b4c4ce5
+config: 9c1bb04af5f147db0da20ac6db06bb18
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/Activity.html b/docs/build/html/Activity.html
@@ -6,7 +6,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Provenance &#8212; Synapse Python Client 2.3.0 documentation</title>
+    <title>Provenance &#8212; Synapse Python Client 2.3.1 documentation</title>
     <link rel="stylesheet" href="_static/custom.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
@@ -46,7 +46,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="Evaluation.html" title="Evaluations"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.1 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Provenance</a></li> 
       </ul>
     </div>  
@@ -243,13 +243,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="Evaluation.html" title="Evaluations"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.1 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Provenance</a></li> 
       </ul>
     </div>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Mar 11, 2021.
+      Last updated on Apr 13, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.1.2.
     </div>
     <script type="text/javascript">

diff --git a/docs/build/html/Annotations.html b/docs/build/html/Annotations.html
@@ -6,7 +6,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Annotations &#8212; Synapse Python Client 2.3.0 documentation</title>
+    <title>Annotations &#8212; Synapse Python Client 2.3.1 documentation</title>
     <link rel="stylesheet" href="_static/custom.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
@@ -46,7 +46,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="Activity.html" title="Provenance"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.1 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Annotations</a></li> 
       </ul>
     </div>  
@@ -197,13 +197,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="Activity.html" title="Provenance"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.1 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Annotations</a></li> 
       </ul>
     </div>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Mar 11, 2021.
+      Last updated on Apr 13, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.1.2.
     </div>
     <script type="text/javascript">

diff --git a/docs/build/html/Client.html b/docs/build/html/Client.html
@@ -6,7 +6,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Synapse Client &#8212; Synapse Python Client 2.3.0 documentation</title>
+    <title>Synapse Client &#8212; Synapse Python Client 2.3.1 documentation</title>
     <link rel="stylesheet" href="_static/custom.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
@@ -46,7 +46,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="S3Storage.html" title="S3 Storage Features"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.1 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Synapse Client</a></li> 
       </ul>
     </div>  
@@ -917,8 +917,6 @@ <h2>Synapse<a class="headerlink" href="#synapse" title="Permalink to this headli
 following fields: email, password, apiKey</p></li>
 <li><p><strong>rememberMe</strong> – Whether the authentication information should be cached in your operating system’s
 credential storage.</p></li>
-<li><p><strong>silent</strong> – Suppress login welcome message</p></li>
-<li><p><strong>forced</strong> – Skip any cached credential lookup</p></li>
 <li><p><strong>authToken</strong> – A bearer authorization token, e.g. a personal access token, can be used in lieu of a
 password or apiKey</p></li>
 </ul>
@@ -1570,13 +1568,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="S3Storage.html" title="S3 Storage Features"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.3.1 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Synapse Client</a></li> 
       </ul>
     </div>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Mar 11, 2021.
+      Last updated on Apr 13, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.1.2.
     </div>
     <script type="text/javascript">