Add pre-commit (#25)

* remove devcontainer

* remove gitignore

* remove temporary files

* remove more temporary files

* rename mlp

* regularize header app files

* change description in setup.cfg

* clean app files

* add note about biosnicar installation

* clean header files

* translate environment conda to pip

* ruff and black formatting

* pre-commit formatting

---------

Co-authored-by: Lou Chevrollier <[email protected]>

.github/scripts/generate_pip_deps_from_conda.py

@@ -0,0 +1,153 @@
+#!/usr/bin/env python3
+"""
+(Copied from pandas:
+https://github.com/pandas-dev/pandas/blob/main/scripts/generate_pip_deps_from_conda.py)
+Convert the conda environment.yml to the pip requirements-dev.txt, or
+check that they have the same packages (for the CI)
+
+Usage:
+
+    Generate `requirements-dev.txt`
+    $ python scripts/generate_pip_deps_from_conda.py
+
+    Compare and fail (exit status != 0) if `requirements-dev.txt` has not been
+    generated with this script:
+    $ python scripts/generate_pip_deps_from_conda.py --compare
+
+"""
+
+import argparse
+import pathlib
+import re
+import sys
+
+if sys.version_info >= (3, 11):
+    pass
+else:
+    pass
+import yaml
+
+EXCLUDE = {"python"}
+REMAP_VERSION = {"tzdata": "2022.1"}
+RENAME = {}
+
+
+def conda_package_to_pip(package: str):
+    """
+    Convert a conda package to its pip equivalent.
+
+    In most cases they are the same, those are the exceptions:
+    - Packages that should be excluded (in `EXCLUDE`)
+    - Packages that should be renamed (in `RENAME`)
+    - A package requiring a specific version, in conda is defined with a single
+      equal (e.g. ``pandas=1.0``) and in pip with two (e.g. ``pandas==1.0``)
+    """
+    package = re.sub("(?<=[^<>])=", "==", package).strip()
+    print(package)
+
+    for compare in ("<=", ">=", "=="):
+        if compare in package:
+            pkg, version = package.split(compare)
+            if pkg in EXCLUDE:
+                return
+            if pkg in REMAP_VERSION:
+                return "".join((pkg, compare, REMAP_VERSION[pkg]))
+            if pkg in RENAME:
+                return "".join((RENAME[pkg], compare, version))
+
+    if package in EXCLUDE:
+        return
+
+    if package in RENAME:
+        return RENAME[package]
+
+    return package
+
+
+def generate_pip_from_conda(
+    conda_path: pathlib.Path, pip_path: pathlib.Path, compare: bool = False
+) -> bool:
+    """
+    Generate the pip dependencies file from the conda file, or compare that
+    they are synchronized (``compare=True``).
+
+    Parameters
+    ----------
+    conda_path : pathlib.Path
+        Path to the conda file with dependencies (e.g. `environment.yml`).
+    pip_path : pathlib.Path
+        Path to the pip file with dependencies (e.g. `requirements-dev.txt`).
+    compare : bool, default False
+        Whether to generate the pip file (``False``) or to compare if the
+        pip file has been generated with this script and the last version
+        of the conda file (``True``).
+
+    Returns
+    -------
+    bool
+        True if the comparison fails, False otherwise
+    """
+    with conda_path.open() as file:
+        deps = yaml.safe_load(file)["dependencies"]
+
+    pip_deps = []
+    for dep in deps:
+        if isinstance(dep, str):
+            conda_dep = conda_package_to_pip(dep)
+            if conda_dep:
+                pip_deps.append(conda_dep)
+        elif isinstance(dep, dict) and len(dep) == 1 and "pip" in dep:
+            pip_deps.extend(dep["pip"])
+        else:
+            raise ValueError(f"Unexpected dependency {dep}")
+
+    header = (
+        f"# This file is auto-generated from {conda_path.name}, do not modify.\n"
+        "# See that file for comments about the need/usage of each dependency.\n\n"
+    )
+    pip_content = header + "\n".join(pip_deps) + "\n"
+
+    # Add setuptools to requirements-dev.txt
+
+    # with open(pathlib.Path(conda_path.parent, "pyproject.toml"), "rb") as fd:
+    #     meta = tomllib.load(fd)
+    # for requirement in meta["build-system"]["requires"]:
+    #     if "setuptools" in requirement:
+    #         pip_content += requirement
+    #         pip_content += "\n"
+
+    if compare:
+        with pip_path.open() as file:
+            return pip_content != file.read()
+
+    with pip_path.open("w") as file:
+        file.write(pip_content)
+    return False
+
+
+if __name__ == "__main__":
+    argparser = argparse.ArgumentParser(
+        description="convert (or compare) conda file to pip"
+    )
+    argparser.add_argument(
+        "--compare",
+        action="store_true",
+        help="compare whether the two files are equivalent",
+    )
+    args = argparser.parse_args()
+
+    conda_fname = "dev-environment.yml"
+    pip_fname = "requirements-dev.txt"
+    repo_path = pathlib.Path(__file__).parent.parent.parent.absolute()
+    res = generate_pip_from_conda(
+        pathlib.Path(repo_path, conda_fname),
+        pathlib.Path(repo_path, pip_fname),
+        compare=args.compare,
+    )
+    if res:
+        msg = (
+            f"`{pip_fname}` has to be generated with `{__file__}` after "
+            f"`{conda_fname}` is modified.\n"
+        )
+        sys.stderr.write(msg)
+    sys.exit(res)

.github/workflows/main.yml

@@ -17,23 +17,23 @@ jobs:
           environment-file: environment.yml
           use-mamba: true
           python-version: "3.9"
-          
+
       - shell: bash -l {0}
         run: |
           conda info
           conda list
-          
+
       - name: Install snowlaps-emulator
         shell: bash -l {0}
         run: |
             pip install -e .
-            
+
       - name: Checkout code
         uses: actions/checkout@v4
         with:
           # Full git history is needed to get a proper list of changed files within `super-linter`
-          fetch-depth: 0 
-          
+          fetch-depth: 0
+
       - name: Run tests and generate coverage report
         shell: bash -l {0}
         run: |
@@ -58,4 +58,3 @@ jobs:
       #     snyk test --file=dev-requirements.txt --package-manager=pip --severity-threshold=high
       #   env:
       #     SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-