issue1/re-org (#2)

- Move docs to a `docs` folder
- Move *.ipynb to a `notebooks` folder
- Move data to a `data` folder
- Move scripts to a `scripts` folder
- Add pyproject.toml
- Create installable package
- Ensures the example data will run using the new package.
- Runs `ruff` on everything and modifies `*.md` files using
  `mdformat
- add custom exception class for file format errors
- add basic test
- add CI testing
- Removed several new and old environment files to lower maintenance
  burden.
  - environment.yaml
  - envs/py3.10-tests.yaml
  - envs/py3.11-tests.yaml
  - envs/py3.12-tests.yaml
- Removal of the environment files required updating the README.md to
  handle creating an environment file for the user.
- We ignore the created environment.yaml file in the .gitignore file
- Removed requirements.txt as all requirements are handled by the
  pyproject.toml file.
- Updated docs to fix URL links.
- Also updated comments in untested code to use correct URLs.
- Refactored the test.yaml workflow.
- Refactored the following to remove extraneous line character
  - tests/test_basic.py (also renamed the method and module to correlate
    with the method being tested in the module.)
  - src/holoseq/exceptions.py
  - pyproject.toml
  - .github/workflows/test.yaml
- make ruff ignore dirs

Resolves #1 
---------

Co-authored-by: Demetris Roumis <[email protected]>

.github/workflows/test.yaml

@@ -0,0 +1,38 @@
+name: Run tests
+on:
+  pull_request:
+  push:
+    branches: [main]
+    paths-ignore:
+      - "docs/"
+      - "notebooks/"
+      - "scripts/"
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        version: ["3.10", "3.11", "3.12"]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev,test]
+
+      - name: Run ruff
+        uses: astral-sh/ruff-action@v2
+
+      - name: Run tests
+        run: |
+          pytest -v tests --cov=src/holoseq --cov-append

.gitignore

@@ -25,6 +25,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+environment.yaml
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-toml
+  - id: check-builtin-literals
+  - id: check-case-conflict
+  - id: check-docstring-first
+  - id: check-illegal-windows-names
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-toml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: no-commit-to-branch
+  - id: pretty-format-json
+  - id: trailing-whitespace
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.8.0
+  hooks:
+    - id: ruff
+      types_or:
+        - python
+        - pyi
+      args:
+        - --fix
+        - --exit-non-zero-on-fix
+    - id: ruff-format
+      types_or:
+        - python
+        - pyi
+
+- repo: https://github.com/executablebooks/mdformat
+  rev: 0.7.19
+  hooks:
+    - id: mdformat
+      types:
+        - markdown
+      language: python
+      args:
+        - --wrap
+        - "100"