Use github cache feature

.github/workflows/document_tutorials.yml

@@ -1,102 +1,44 @@
-name: Convert Tutorial Files
-
+name: autogenerate docs from tutorials
+# Not finished! Only will run on a specific branch for now so can be left
 on:
+  # Triggers the workflow on push but only for the main branch
   push:
-    branches: [documentation]
+    branches: [ workflow_trials ]
+    paths: ['**.ipynb']
 
 jobs:
-  build:
-    runs-on: ubuntu-latest  # You can specify a different runner if needed
-
+  docs-from-tutorials:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v3
-
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.8  # Specify the Python version you need
-
-    - name: Install dependencies
-      run: pip install jupyter nbconvert
-
-    - name: Run Conversion Script
-      uses: jannekem/run-python-script-action@v1
-      with:
-        script: |
-            import pathlib
-            import shutil
-            import subprocess
-
-            def create_new_directory_with_modified_files(directory_path, new_directory_path):
-                try:
-                    # Create a Path object for the source directory
-                    source_directory = pathlib.Path(directory_path)
-
-                    # Ensure the source directory exists
-                    if not source_directory.is_dir():
-                        raise FileNotFoundError(f"The source directory '{directory_path}' does not exist.")
-
-                    # Create a Path object for the new directory
-                    new_directory = pathlib.Path(new_directory_path)
-
-                    # Create the new directory if it doesn't exist
-                    new_directory.mkdir(parents=True, exist_ok=True)
-
-                    # Loop through files in the source directory
-                    for file_path in source_directory.iterdir():
-                        if file_path.is_file():
-                            # Remove spaces and change hyphens to underscores in the filename
-                            new_name = file_path.name.replace(' ', '').replace('-', '_')
-
-                            # Construct the path for the new file in the new directory
-                            new_file_path = new_directory / new_name
-
-                            # Copy the file to the new directory with the modified name
-                            shutil.copy2(file_path, new_file_path)
-
-                            print(f"Copied '{file_path}' to '{new_file_path}'")
-
-                    print("File copying completed successfully.")
-
-
-                except Exception as e:
-                    print(f"An error occurred: {str(e)}")
-
-            def convert_ipynb_to_rst(directory_path):
-                try:
-                    # Create a Path object for the directory
-                    directory = pathlib.Path(directory_path)
-
-                    # Ensure the directory exists
-                    if not directory.is_dir():
-                        raise FileNotFoundError(f"The directory '{directory_path}' does not exist.")
-
-                    # Loop through files in the directory
-                    for file_path in directory.iterdir():
-                        if file_path.is_file() and file_path.suffix == '.ipynb':
-                            # Construct the command to run nbconvert
-                            command = f"jupyter nbconvert --to rst {str(file_path)}"
-
-                            # Run nbconvert using subprocess
-                            subprocess.run(command, shell=True, check=True)
-
-                            print(f"Converted '{file_path}' to .rst")
-
-                    print("Conversion to .rst completed successfully.")
-
-                except Exception as e:
-                    print(f"An error occurred during conversion: {str(e)}")
-
-            if __name__ == "__main__":
-                # Specify the source directory path where you want to process files
-                source_directory_path = "tutorial/"
-
-                # Specify the new directory path where you want to create modified files
-                new_directory_path = "docs/tutorial"
-
-                # Call the function to create a new directory with modified filenames
-                create_new_directory_with_modified_files(source_directory_path, new_directory_path)
-
-                # Run nbconvert to convert .ipynb files to .rst in the new directory
-                convert_ipynb_to_rst(new_directory_path)
+      #  Check out repo and set up Python
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      #
+      - name: run python script after setting up
+        run: |
+          poetry run pip install nbconvert
+          poetry install
+          mkdir tutorial
+          poetry run python renaming.py
+
+      - name: remove notebooks from docs
+        run: rm *.ipynb
+
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          default_author: github_actions
+          message: 'Updating tutorial rsts for docs'
+          add: 'sed/docs/tutorial/'

.github/workflows/pylint.yml

@@ -1,6 +1,6 @@
 # This workflow will install Python dependencies, lint and run tests with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
+# TODO: switch to the cached version
 name: linting
 
 on: [push]

.github/workflows/testing.yml

@@ -0,0 +1,38 @@
+name: pytest
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pytest:
+    # Using matrix strategy
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    runs-on: ubuntu-latest
+    steps:
+      #-------------------------------------#
+      #  Check out repo and set up Python   #
+      #-------------------------------------#
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: ${{matrix.python-version}}
+          poetry-version: 1.2.2
+
+      #------------------------#
+      #  Run pytest   #
+      #------------------------#
+      - name: Run tests
+        run: |
+          poetry run pytest
+
+      # Coveralls missing

.github/workflows/update_requirements.yml

@@ -0,0 +1,34 @@
+name: update requirements.txt
+
+on:
+  # Triggers the workflow on push but only for the main branch
+  push:
+    branches: [ main ]
+    paths: [pyproject.toml]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      #  Check out repo and set up Python
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      #  Generates and commits a requirements.txt used by readthedocs
+      - name: Export requirements.txt
+        run: poetry export --without-hashes --format=requirements.txt -o docs/requirements.txt -E docs -E notebook
+
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          default_author: github_actions
+          message: 'Updating requirements for docs'
+          add: 'docs/requirements.txt'