Merge pull request #2118 from PrincetonUniversity/devel

Devel

.appveyor.yml

@@ -0,0 +1,54 @@
+version: '{build}'
+branches:
+  except:
+  - gh-pages
+skip_tags: true
+skip_branch_with_pr: true
+clone_depth: 15
+image: Ubuntu2004
+environment:
+  PIP_PROGRESS_BAR: off
+  APPVEYOR_CONSOLE_DISABLE_PTY: true
+  OMP_NUM_THREADS: 1
+  OPENBLAS_NUM_THREADS: 1
+  matrix:
+  - PYTHON: python3.8
+
+init:
+- ps: |
+    sudo apt-get update
+    sudo apt-get install -y --no-install-recommends build-essential graphviz git curl $Env:PYTHON-dev $Env:PYTHON-distutils $Env:PYTHON-venv
+    sudo update-alternatives --install /usr/bin/python python /usr/bin/$Env:PYTHON 10
+    sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/$Env:PYTHON 10
+    sudo update-alternatives --set python /usr/bin/$Env:PYTHON
+    sudo update-alternatives --set python3 /usr/bin/$Env:PYTHON
+
+install:
+- ps: |
+    python -m venv venv
+    venv/bin/Activate.ps1
+    echo "#!/bin/sh" > venv/bin/xdg-open
+    chmod +x venv/bin/xdg-open
+
+    pip --version
+    pip install -U pip wheel cython
+    pip install -U coveralls
+    pip install -U -e .[dev]
+
+build: off
+
+test_script:
+- ps: |
+    if (Test-Path Env:\COVERALLS_REPO_TOKEN ) {
+      $Env:COV="--cov=psyneulink"
+    }
+    python -m pytest --junit-xml=tests_out.xml $Env:COV --verbosity=0 --capture=sys -o console_output_style=count
+
+on_success:
+- ps: |
+    if (Test-Path Env:\COVERALLS_REPO_TOKEN ) {
+      coveralls
+    }
+
+on_finish:
+- ps: curl -X POST -F "file=@tests_out.xml" https://ci.appveyor.com/api/testresults/junit/$Env:APPVEYOR_JOB_ID

.github/workflows/compare-comment.yml

@@ -16,7 +16,7 @@ jobs:
 
     - name: 'Download docs artifacts'
       id: docs-artifacts
-      uses: actions/github-script@v4.0.2
+      uses: actions/github-script@v4.1
       with:
         script: |
           var artifacts = await github.actions.listWorkflowRunArtifacts({
@@ -32,11 +32,14 @@ jobs:
           core.setOutput('DOCS_GEN_ENV', docsSuffix);
 
           var docsArtifacts = artifacts.data.artifacts.filter((artifact) => {
-            return artifact.name.endsWith(docsSuffix) && artifact.name.startsWith('Documentation-')
+            return (
+              (artifact.name.endsWith(docsSuffix) && artifact.name.startsWith('Documentation-'))
+              || artifact.name == 'pr_number'
+            )
           });
 
-          // check that we got exactly 2 artifacts
-          console.assert(docsArtifacts.length == 2, docsSuffix, docsArtifacts, artifacts.data.artifacts);
+          // check that we got exactly 3 artifacts
+          console.assert(docsArtifacts.length == 3, docsSuffix, docsArtifacts, artifacts.data.artifacts);
 
           var fs = require('fs');
           for (artifact of docsArtifacts) {
@@ -55,6 +58,7 @@ jobs:
       run: |
         unzip Documentation-base-*.zip -d docs-base/
         unzip Documentation-head-*.zip -d docs-head/
+        unzip pr_number.zip
 
     - name: Compare
       shell: bash
@@ -64,16 +68,17 @@ jobs:
         (diff -r docs-base docs-head && echo 'No differences!' || true) | tee ./result.diff
 
     - name: Post comment with docs diff
-      uses: actions/github-script@v4.0.2
+      uses: actions/github-script@v4.1
       with:
         script: |
           var fs = require('fs');
           var text = fs.readFileSync("./result.diff").slice(0,16384);
+          var issue_number = Number(fs.readFileSync('./pr_number.txt'));
 
-          console.log('Posting diff to PR: ${{ github.event.workflow_run.pull_requests[0].number }}')
+          console.log('Posting diff to PR: ' + issue_number);
 
           github.issues.createComment({
-            issue_number: ${{ github.event.workflow_run.pull_requests[0].number }},
+            issue_number: issue_number,
             owner: context.repo.owner,
             repo: context.repo.repo,
             body: 'This PR causes the following changes to the html docs (${{ steps.docs-artifacts.outputs.DOCS_GEN_ENV }}):\n```\n' + text + '\n...\n```\nSee CI logs for the full diff.'

.github/workflows/pnl-ci-docs.yml

@@ -94,14 +94,26 @@ jobs:
       run: git tag 'v999.999.999.999'
 
     - name: Build Documentation
-      run: sphinx-build -b html -aE -j auto docs/source pnl-html
+      run: make -C docs/ html -e SPHINXOPTS="-aE -j auto"
 
     - name: Upload Documentation
       uses: actions/upload-artifact@v2.2.4
       with:
         name: Documentation-${{matrix.pnl-version}}-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         retention-days: 1
-        path: pnl-html
+        path: docs/build/html
+
+    - name: Store PR number
+      if: ${{ github.event_name == 'pull_request' }}
+      run: echo ${{ github.event.pull_request.number }} > ./pr_number.txt
+
+    - name: Upload PR number for other workflows
+      if: ${{ github.event_name == 'pull_request' }}
+      uses: actions/upload-artifact@v2.2.4
+      with:
+          name: pr_number
+          path: ./pr_number.txt
+
 
   docs-deploy:
     strategy:

.github/workflows/prepare-release.yml

@@ -22,7 +22,7 @@ jobs:
         branch: master
 
     - name: Check for existing release with the reference tag
-      uses: actions/github-script@v4
+      uses: actions/github-script@v4.1
       id: exist_check
       with:
         script: |
@@ -47,7 +47,7 @@ jobs:
           }
 
     - name: Create Release
-      uses: actions/github-script@v4
+      uses: actions/github-script@v4.1
       if: steps.on_master.outputs.on-branch == 'master' && steps.exist_check.outputs.exists == 'no'
       with:
         # We need custom token since the default one doesn't trigger actions

.github/workflows/test-release.yml

@@ -180,7 +180,7 @@ jobs:
         TWINE_REPOSITORY: ${{ secrets.TWINE_REPOSITORY }}
 
     - name: Upload dist files to release
-      uses: actions/github-script@v4
+      uses: actions/github-script@v4.1
       with:
         script: |
           const fs = require('fs')

conftest.py

@@ -118,7 +118,7 @@ def get_func_execution(func, func_mode):
     elif func_mode == 'Python':
         return func.function
     else:
-        assert False, "Unknown function mode: {}".format(mode)
+        assert False, "Unknown function mode: {}".format(mech_mode)
 
 @pytest.helpers.register
 def get_mech_execution(mech, mech_mode):
@@ -132,7 +132,7 @@ def mech_wrapper(x):
             return mech.output_values
         return mech_wrapper
     else:
-        assert False, "Unknown mechanism mode: {}".format(mode)
+        assert False, "Unknown mechanism mode: {}".format(mech_mode)
 
 @pytest.helpers.register
 def expand_np_ndarray(arr):

dev_requirements.txt

@@ -1,5 +1,5 @@
 jupyter<=1.0.0
-pytest<6.2.5
+pytest<6.2.6
 pytest-benchmark<3.4.2
 pytest-cov<2.12.2
 pytest-helpers-namespace<2021.4.30