Add basic cli interface to scripts (#5)

.github/workflows/build.yml

@@ -0,0 +1,24 @@
+# This workflow builds and checks the package for release
+name: Build
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - run: pip install tox
+
+    - name: Test build integrity
+      run: tox -e build
+      env:
+        # Use the CPU only version of torch when building/running the code
+        PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - run: pip install tox
+
+    - name: Lint the code
+      run: tox -e lint

.github/workflows/tests.yml

@@ -4,57 +4,39 @@ on:
   push:
     branches: [main]
   pull_request:
-    # Run for all PRs
+    # Check all PR
 
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
-    name: Test on ${{ matrix.os }}
     strategy:
       matrix:
         include:
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
+            python-version: "3.8"
+          - os: ubuntu-22.04
+            python-version: "3.11"
           - os: macos-11
+            python-version: "3.11"
           - os: windows-2019
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-
-      - name: install tests dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox
+           python-version: "3.11"
 
-      - name: run Python tests
-        run: python -m tox
-        env:
-          PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
-
-  # check that we can build Python wheels on any Python version
-  python-build:
-    runs-on: ubuntu-20.04
-    name: check Python build
-    strategy:
-      matrix:
-        python-version: ['3.7', '3.11']
     steps:
-      - uses: actions/checkout@v3
-
-      - name: set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: install python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox wheel
-
-      - name: python build tests
-        run: tox -e build-python
-        env:
-          PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - run: pip install tox
+
+    - name: run Python tests
+      run: tox -e tests
+      env:
+        # Use the CPU only version of torch when building/running the code
+        PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+
+    - name: Upload codecoverage
+      uses: codecov/codecov-action@v3
+      with:
+        files: ./tests/coverage.xml

pyproject.toml

@@ -42,7 +42,7 @@ repository = "https://github.com/lab-cosmo/metatensor-models"
 # changelog = "TODO"
 
 [project.scripts]
-maicos = "maicos.__main__:main"
+metatensor_models = "metatensor_models.__main__:main"
 
 ### ======================================================================== ###
 
@@ -59,7 +59,7 @@ soap-bpnn = [
 ]
 
 [tool.setuptools.packages.find]
-where = ["src", "bin"]
+where = ["src"]
 
 [tool.setuptools.dynamic]
 version = {attr = "metatensor_models.__version__"}

src/metatensor_models/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.0-dev"
+__version__ = "2023.11.29"

src/metatensor_models/__main__.py

@@ -0,0 +1,72 @@
+"""The main entry point for the metatensor model interface."""
+import argparse
+import sys
+
+from . import __version__
+from .scripts import evaluate, export, train
+
+
+def main():
+    ap = argparse.ArgumentParser(
+        description=__doc__,
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    ap.add_argument(
+        "--version",
+        action="version",
+        version=f"metatensor_models {__version__}",
+    )
+
+    ap.add_argument(
+        "--debug",
+        action="store_true",
+        help="Run with debug options.",
+    )
+
+    ap.add_argument(
+        "--logfile", dest="logfile", action="store", help="Logfile (optional)"
+    )
+
+    subparser = ap.add_subparsers(help="sub-command help")
+    evaluate_parser = subparser.add_parser(
+        "evaluate",
+        help=evaluate.__doc__,
+        description="evaluate",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    evaluate_parser.set_defaults(callable="evaluate")
+
+    export_parser = subparser.add_parser(
+        "export",
+        help=export.__doc__,
+        description="export",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    export_parser.set_defaults(callable="export")
+    train_parser = subparser.add_parser(
+        "train",
+        help=train.__doc__,
+        description="train",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    train_parser.set_defaults(callable="train")
+
+    if len(sys.argv) < 2:
+        ap.error("A subcommand is required.")
+
+    # Be case insensitive for the subcommand
+    sys.argv[1] = sys.argv[1].lower()
+
+    args = ap.parse_args(sys.argv[1:])
+
+    if args.callable == "evaluate":
+        evaluate()
+    elif args.callable == "export":
+        export()
+    elif args.callable == "train":
+        train()
+
+
+if __name__ == "__main__":
+    main()

src/metatensor_models/scripts/__init__.py

@@ -0,0 +1,5 @@
+from .evaluate import evaluate
+from .export import export
+from .train import train
+
+__all__ = ["evaluate", "export", "train"]

src/metatensor_models/scripts/evaluate.py

@@ -0,0 +1,3 @@
+def evaluate():
+    """evaluate a model"""
+    print("Run evaluate...")

src/metatensor_models/scripts/export.py

@@ -0,0 +1,3 @@
+def export():
+    """export a model"""
+    print("Run exort...")

src/metatensor_models/scripts/train.py

@@ -0,0 +1,3 @@
+def train():
+    """train a model"""
+    print("Run train...")

tests/cli.py

@@ -0,0 +1,30 @@
+import subprocess
+import sys
+
+import pytest
+
+from metatensor_models.scripts import __all__ as available_scripts
+
+
+class Test_parse_args(object):
+    """Tests for argument parsing."""
+
+    def test_required_args(self):
+        """Test required arguments."""
+        with pytest.raises(subprocess.CalledProcessError):
+            subprocess.check_call(["metatensor_models"])
+
+    def test_wrong_module(self):
+        """Test wrong module."""
+        with pytest.raises(subprocess.CalledProcessError):
+            subprocess.check_call(["metatensor_models", "foo"])
+
+    @pytest.mark.parametrize("module", tuple(available_scripts))
+    def test_available_modules(self, module):
+        """Test available modules."""
+        subprocess.check_call(["metatensor_models", module, "--help"])
+
+    @pytest.mark.parametrize("args", ("version", "help"))
+    def test_extra_options(self, args):
+        """Test extra options."""
+        subprocess.check_call(["metatensor_models", "--" + args])

tox.ini

@@ -12,8 +12,7 @@ passenv = *
 lint_folders = "{toxinidir}/src"
 
 [testenv:lint]
-# this environement lints the Python code with flake8 (code linter), black (code
-# formatter), and isort (sorting of imports)
+description = Run linters and type checks
 package = skip
 deps =
     flake8
@@ -29,9 +28,7 @@ commands =
     isort --check-only --diff {[testenv]lint_folders}
 
 [testenv:format]
-# this environement abuses tox to do actual formatting
-#
-# Users can run `tox -e format` to run formatting on all files
+description = Abuse tox to do actual formatting on all files.
 package = skip
 deps =
     black
@@ -51,34 +48,21 @@ deps =
 commands =
     pytest --import-mode=append {posargs}
 
-[testenv:soap-bpnn]
-passenv = *
-deps =
-    pytest
-
-commands =
-    echo "success"
-
-[testenv:build-python]
-# this environement makes sure one can build sdist and wheels for Python
+[testenv:build]
+description = builds the package and checks integrity
+usedevelop = true
 deps =
-    setuptools
-    wheel
-    cmake
-    twine
     build
-
-allowlist_externals =
-    bash
-
+    check-manifest
+    twine
+allowlist_externals = bash
+commands_pre =
+    bash -c "if [ -e {toxinidir}/dist/*tar.gz ]; then unlink {toxinidir}/dist/*.whl; fi"
+    bash -c "if [ -e {toxinidir}/dist/*tar.gz ]; then unlink {toxinidir}/dist/*.tar.gz; fi"
 commands =
-    # check building sdist and wheels from a checkout
     python -m build
-    twine check dist/*.tar.gz
-    twine check dist/*.whl
-
-    # check building wheels from the sdist
-    bash -c "python -m pip wheel --verbose dist/metatensor_models-*.tar.gz -w dist/test"
+    twine check dist/*.tar.gz dist/*.whl
+    check-manifest {toxinidir}
 
 [flake8]
 # longer lines for compatibility with other linters