Update main dimelo repo to v0.2.0

.github/workflows/formatting.yml

@@ -0,0 +1,19 @@
+name: dimelo-formatting
+on: [ pull_request ]
+jobs:
+  ruff-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          version: 0.6.8
+  # TODO: Is it really necessary for these to be separate jobs? This seems redundant.
+  ruff-format-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          version: 0.6.8
+          args: 'format --check'

.github/workflows/test.yml

@@ -1,65 +1,42 @@
-name: dimelo
+name: dimelo-test
 
-on: [push]
+on: 
+  workflow_dispatch:  # Allows manual trigger of the workflow
+  pull_request:  # Trigger by default on PR opened, reopened, or synchronized (commits pushed to PR)
 
 jobs:
-  build-conda:
-    runs-on: ubuntu-latest
+  platform_matrix:  # Run the tests on each supported platform
     strategy:
       matrix:
-        python-version: ["3.7"]
-
+        platform:  # Define the platform tag and the file name of the appropriate miniconda install script
+          - os: ubuntu-latest
+            miniconda: Miniconda3-latest-Linux-x86_64.sh
+          - os: macos-latest
+            miniconda: Miniconda3-latest-MacOSX-x86_64.sh
+    runs-on: ${{ matrix.platform.os }}
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
-        with:
-          python-version: ${{ matrix.python-version }}
-      # TODO: If we change the name of the dimelo subdirectory, conda install as written here should break.
-      # Installing format dependencies with pip for full compatibility
-      - name: Install dependencies
-        run: |
-          $CONDA/bin/conda env update --file environment_linux.yml --name base
-          pip install flake8 black isort
-          $CONDA/bin/conda install pytest
-      - name: Lint with flake8
-        run: |
-          flake8
-      - name: Check format with black
-        run: |
-          black --config pyproject.toml --diff --check .
-      - name: Clean up and sort imports
-        run: |
-          isort --check-only .
-      - name: Test with pytest
-        run: |
-          $CONDA/bin/pytest
-
-  build-pip:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.7"]
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 black isort pytest
+      - uses: actions/checkout@v4
+      - name: Setup conda and run pytest
+        run: |
+          # Install Miniconda if not available on the runner
+          wget https://repo.anaconda.com/miniconda/${{ matrix.platform.miniconda }} -O miniconda.sh
+          bash miniconda.sh -b -p $HOME/miniconda
+          source $HOME/miniconda/etc/profile.d/conda.sh
+
+          # Create conda environment from environment.yml
+          conda env create -f environment.yml
+
+          # Activate the environment
+          conda activate $(head -n 1 environment.yml | cut -d' ' -f2)
+
+          # Install pip dependencies and the package itself
           pip install .
-      - name: Lint with flake8
-        run: |
-          flake8
-      - name: Check format with black
-        run: |
-          black --diff --check .
-      - name: Clean up and sort imports
-        run: |
-          isort --check-only .
-      - name: Test with pytest
-        run: |
+
+          # Additional testing dependencies not covered in environment.yml
+          conda install pytest
+
+          # Make sure everything is installed correctly
+          conda list
+
+          # Run pytest
           pytest

.gitignore

@@ -53,4 +53,12 @@ coverage.xml
 .pytest_cache/
 
 # Sphinx documentation
-docs/_build/
+docs/_build/
+
+
+# Ignore tutorial output files
+dimelo/test/output
+
+# Checkpoint files
+.ipynb_checkpoints/
+

.pre-commit-config.yaml

@@ -1,15 +1,16 @@
 repos:
-    - repo: https://github.com/psf/black
-      rev: 22.3.0
-      hooks:
-          - id: black
-    - repo: https://gitlab.com/pycqa/flake8
-      rev: 3.9.2
-      hooks:
-          - id: flake8
-    - repo: https://github.com/pycqa/isort
-      rev: 5.9.3
-      hooks:
-          - id: isort
-            name: isort (python)
-            additional_dependencies: [toml]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.8
+  hooks:
+    # Run the linter.
+    - id: ruff
+    # Run the formatter.
+    - id: ruff-format
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: v1.9.0
+#   hooks:
+#     - id: mypy
+      # These are things I'm considering including in the ignore list, but should think about...
+      # Ignore missing import errors caused by pre-commit being run in an isolated environment
+      # Allow conflicting assignment to existing variables in reasonable circumstances; mainly for coersion of path strings
+      # args: [--ignore-missing-imports, --allow-redefinition]