v0.3.0 Merge pull request #10 from McIntosh-Lab/staging

Merge v0.3.0 changes into main

.bandit.yml

@@ -0,0 +1,4 @@
+exclude_dirs:
+  - plspy/_version.py
+  - versioneer.py
+  - plspy/tests

.circleci/config.yml

@@ -14,9 +14,10 @@ orbs:
 # Define a job to be invoked later in a workflow.
 # See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
-  build-and-test: 
+  build-and-test-3_10:
     docker:
       - image: cimg/python:3.10.2
+    resource_class: medium
     steps:
       - checkout
       - python/install-packages:
@@ -25,26 +26,109 @@ jobs:
       - run:
           name: Run tests
           command: pytest
-  build-docs: 
+  build-and-test-3_9:
+    docker:
+      - image: cimg/python:3.9
+    resource_class: medium
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: pip
+          pip-dependency-file: requirements.txt
+      - run:
+          name: Run tests
+          command: pytest
+  build-and-test-3_8:
+    docker:
+      - image: cimg/python:3.8
+    resource_class: medium
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: pip
+          pip-dependency-file: requirements.txt
+      - run:
+          name: Run tests
+          command: pytest
+  build-and-test-3_7:
+    docker:
+      - image: cimg/python:3.7
+    resource_class: medium
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: pip
+          pip-dependency-file: requirements.txt
+      - run:
+          name: Run tests
+          command: pytest
+  build-docs:
     docker:
       - image: cimg/python:3.10.2
+    resource_class: medium
     steps:
       - checkout
       - python/install-packages:
           pkg-manager: pip
           pip-dependency-file: requirements_dev.txt
       - run:
-          name: build documentation 
+          name: build documentation
           command: |
             cd docs
             sphinx-build -M html . _build
-
+  test_pypi_publish-3_10:
+    docker:
+      - image: circleci/python:3.10
+    steps:
+      - checkout  # checkout source code to working directory
+      - run:
+          command: |  # create whl, install twine and publish to Test PyPI
+            python setup.py sdist bdist_wheel
+            sudo pip install pipenv
+            pipenv install twine
+            pipenv run twine upload --repository testpypi dist/* -u __token__ -p $TEST_PYPI_TOKEN
+  pypi_publish-3_10:
+    docker:
+      - image: circleci/python:3.10
+    steps:
+      - checkout  # checkout source code to working directory
+      - run:
+          command: |  # create whl, install twine and publish to PyPI
+            python setup.py sdist bdist_wheel
+            sudo pip install pipenv
+            pipenv install twine
+            pipenv run twine upload dist/* -u __token__ -p $PYPI_TOKEN
 # Invoke jobs via workflows
 # See: https://circleci.com/docs/2.0/configuration-reference/#workflows
 workflows:
   run-tests-and-build-docs:
     # Inside the workflow, you define the jobs you want to run.
     jobs:
-      - build-and-test
+      - build-and-test-3_10
+      - build-and-test-3_9
+      - build-and-test-3_8
+      - build-and-test-3_7
       - build-docs
+      - test_pypi_publish-3_10:
+          requires:
+            - build-and-test-3_10
+            - build-and-test-3_9
+            - build-and-test-3_8
+            - build-and-test-3_7
+            - build-docs
+          filters:
+            branches:
+              only:
+                - staging
 
+      - pypi_publish-3_10:
+          requires:
+            - build-and-test-3_10
+            - build-and-test-3_9
+            - build-and-test-3_8
+            - build-and-test-3_7
+            - build-docs
+          filters:
+            branches:
+              only:
+                - main

.cspell.json

@@ -0,0 +1,15 @@
+{
+  "ignorePaths": [
+    "**/node_modules/**",
+    "**/vscode-extension/**",
+    "**/.git/**",
+    ".vscode",
+    "megalinter",
+    "package-lock.json",
+    "report"
+  ],
+  "language": "en",
+  "noConfigSearch": true,
+  "words": [],
+  "version": "0.2"
+}

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.github/ISSUE_TEMPLATE.md

@@ -2,7 +2,7 @@
 <!-- If you're filing anything other than an issue, feel free to disregard this template-->
 <!-- Assign a label and a Project (please use plspy-board) on the right side of the page-->
 
-### Reproducing code example:
+### Reproducing code example
 
 <!-- A short code example that reproduces the problem/missing feature. It should be
 self-contained, i.e., possible to run as-is via 'python myproblem.py' -->
@@ -14,10 +14,10 @@ import plspy
 
 <!-- Remove these sections for a feature request -->
 
-### Error message:
+### Error message
 
 <!-- Full error message, if any (starting from line Traceback: ...) -->
 
-### plspy/Python version information:
+### plspy/Python version information
 
 <!-- Output from 'import sys, plspy; print(plspy.__version__, sys.version)' -->

.github/workflows/mega-linter.yml

@@ -0,0 +1,82 @@
+---
+# MegaLinter GitHub Action configuration file
+# More info at https://megalinter.github.io
+name: MegaLinter
+
+on:
+  # Trigger mega-linter at every push. Action will also be visible from Pull Requests to master
+  push: # Comment this line to trigger action only on pull-requests (not recommended if you don't pay for GH Actions)
+  pull_request:
+    branches: [master, main]
+
+# env: # Comment env block if you do not want to apply fixes
+  # Apply linter fixes configuration
+  # APPLY_FIXES: all # When active, APPLY_FIXES must also be defined as environment variable (in github/workflows/mega-linter.yml or other CI tool)
+  # APPLY_FIXES_EVENT: pull_request # Decide which event triggers application of fixes in a commit or a PR (pull_request, push, all)
+  # APPLY_FIXES_MODE: commit # If APPLY_FIXES is used, defines if the fixes are directly committed (commit) or posted in a PR (pull_request)
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: MegaLinter
+    runs-on: ubuntu-latest
+    steps:
+      # Git Checkout
+      - name: Checkout Code
+        uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
+          fetch-depth: 0
+
+      # MegaLinter
+      - name: MegaLinter
+        id: ml
+        # You can override MegaLinter flavor used to have faster performances
+        # More info at https://megalinter.github.io/flavors/
+        uses: megalinter/megalinter/flavors/python@v5
+        env:
+          # All available variables are described in documentation
+          # https://megalinter.github.io/configuration/
+          VALIDATE_ALL_CODEBASE: true # Set ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} to validate only diff with main branch
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # ADD YOUR CUSTOM ENV VARIABLES HERE TO OVERRIDE VALUES OF .mega-linter.yml AT THE ROOT OF YOUR REPOSITORY
+
+      # Upload MegaLinter artifacts
+      - name: Archive production artifacts
+        if: ${{ success() }} || ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: MegaLinter reports
+          path: |
+            report
+            mega-linter.log
+
+      # Create pull request if applicable (for now works only on PR from same repository, not from forks)
+      - name: Create Pull Request with applied fixes
+        id: cpr
+        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')
+        uses: peter-evans/create-pull-request@v4
+        with:
+          token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
+          commit-message: "[MegaLinter] Apply linters automatic fixes"
+          title: "[MegaLinter] Apply linters automatic fixes"
+          labels: bot
+      - name: Create PR output
+        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"
+
+      # Push new commit if applicable (for now works only on PR from same repository, not from forks)
+      - name: Prepare commit
+        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'commit' && github.ref != 'refs/heads/main' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')
+        run: sudo chown -Rc $UID .git/
+      - name: Commit and push applied linter fixes
+        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'commit' && github.ref != 'refs/heads/main' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          branch: ${{ github.event.pull_request.head.ref || github.head_ref || github.ref }}
+          commit_message: "[MegaLinter] Apply linters fixes"

.github/workflows/sphinx_docs_to_gh_pages.yaml

@@ -18,8 +18,8 @@ jobs:
       - name: Make conda environment
         uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.9    # Python version to build the html sphinx documentation
-          environment-file: devtools/conda-envs/docs_env.yaml    # Path to the documentation conda environment
+          python-version: 3.9 # Python version to build the html sphinx documentation
+          environment-file: devtools/conda-envs/docs_env.yaml # Path to the documentation conda environment
           auto-update-conda: false
           auto-activate-base: false
           show-channel-urls: true
@@ -32,4 +32,4 @@ jobs:
         with:
           branch: main
           dir_docs: docs
-          sphinxopts: ''
+          sphinxopts: ""

.gitignore

@@ -1,16 +1,22 @@
 __pycache__/
 plspy/__pycache__/
 *.py[cod]
-plspy/.*.py[cod]
-plspy/.*.sw[op]
+plspy/*/.*.py[cod]
+plspy/.*.sw[a-z]
+plspy/io/.*.sw[a-z]
+plspy/core/.*.sw[a-z]
+plspy/visualize/.*.sw[a-z]
+plspy/tests/.*.sw[a-z]
 plspy/.nfs*
 
+report/*
+
 example_*/
 *-info/
 target/
 .tox/
 .pre-commit*
-
+.coverage
 
 build/
 dist/

.jscpd.json

@@ -0,0 +1,15 @@
+{
+  "threshold": 0,
+  "reporters": ["html", "markdown"],
+  "ignore": [
+    "**/node_modules/**",
+    "**/.git/**",
+    "**/.rbenv/**",
+    "**/.venv/**",
+    "**/*cache*/**",
+    "**/.github/**",
+    "**/.idea/**",
+    "**/report/**",
+    "**/*.svg"
+  ]
+}

.mega-linter.yml

@@ -0,0 +1,29 @@
+# Configuration file for MegaLinter
+# See all available variables at https://megalinter.github.io/configuration/ and in linters documentation
+
+APPLY_FIXES: all # all, none, or list of linter keys
+# ENABLE: # If you use ENABLE variable, all other languages/formats/tooling-formats will be disabled by default
+ENABLE_LINTERS: # If you use ENABLE_LINTERS variable, all other linters will be disabled by default
+  - PYTHON_PYLINT
+  - PYTHON_BLACK
+  - PYTHON_FLAKE8
+  - PYTHON_ISORT
+  - PYTHON_BANDIT
+  - PYTHON_MYPY
+  - JSON
+  - MARKDOWN
+  - SPELL_MISSPELL
+# DISABLE:
+# - COPYPASTE # Uncomment to disable checks of excessive copy-pastes
+# - SPELL # Uncomment to disable checks of spelling mistakes
+SHOW_ELAPSED_TIME: true
+FILEIO_REPORTER: false
+DEFAULT_WORKSPACE: "~/.mega-linter/lint"
+DISABLE_ERRORS: true # Uncomment if you want MegaLinter to detect errors but not block CI to pass
+
+ADDITIONAL_EXCLUDED_DIRECTORIES:
+  - build
+  - dist
+  - docs
+  - devtools
+  - report