Use uv lockfile and dependencies in pyproject.toml (#13)

.github/workflows/test.yml

@@ -21,10 +21,14 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v5
 
+            - name: Install the latest version of uv
+              uses: astral-sh/setup-uv@v5
+
             - name: Install artisatomic
               run: |
-                  python3 -m pip install uv
-                  python3 -m uv pip install --editable .
+                  uv sync --frozen
+                  source .venv/bin/activate
+                  uv pip install --compile-bytecode --editable .[dev]
 
             - name: Run Ruff
               if: always()
@@ -42,7 +46,18 @@ jobs:
 
             - name: Lint with mypy
               run: |
-                  mypy --install-types --non-interactive
+                  uv run --frozen mypy --install-types --non-interactive
+
+            - name: Cache pre-commit
+              uses: actions/cache@v4
+              with:
+                  path: ~/.cache/pre-commit
+                  key: pre-commit-3|${{ hashFiles('.pre-commit-config.yaml') }}
+
+            - name: Run pre-commit
+              run: |
+                  source .venv/bin/activate
+                  uv run --frozen -- pre-commit run --all-files --show-diff-on-failure --color=always
 
     pytest:
         runs-on: macos-15
@@ -55,10 +70,13 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v5
 
+            - name: Install the latest version of uv
+              uses: astral-sh/setup-uv@v5
+
             - name: Install artisatomic
               run: |
-                  python3 -m pip install uv
-                  python3 -m uv pip install --compile-bytecode --editable .
+                  uv sync --frozen
+                  uv pip install --compile-bytecode --editable .[dev]
 
             - name: Cache CMFGEN atomic data
               uses: actions/cache@v4
@@ -72,7 +90,7 @@ jobs:
               run: source ./setup_cmfgen_data.sh
 
             - name: Test with pytest
-              run: pytest
+              run: uv run --frozen python3 -m pytest
 
     tests:
         strategy:
@@ -93,10 +111,13 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v5
 
+            - name: Install the latest version of uv
+              uses: astral-sh/setup-uv@v5
+
             - name: Install artisatomic
               run: |
-                  python3 -m pip install uv
-                  python3 -m uv pip install --compile-bytecode --editable .
+                  uv sync --frozen
+                  uv pip install --compile-bytecode --editable .[dev]
 
             - name: Cache CMFGEN atomic data
               uses: actions/cache@v4
@@ -130,7 +151,7 @@ jobs:
             - name: Generate artis atomic data files
               run: |
                   cp tests/${{ matrix.testname }}/artisatomicionhandlers.json .
-                  makeartisatomicfiles -output_folder tests/${{ matrix.testname }}/output
+                  uv run --frozen makeartisatomicfiles -output_folder tests/${{ matrix.testname }}/output
 
             - name: Checksum output files
               working-directory: tests/${{ matrix.testname }}/output

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
       hooks:
           - id: yamlfmt
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.8.3
+      rev: v0.9.1
       hooks:
           - id: ruff
             args: [--fix]

README.md

@@ -6,15 +6,22 @@
 First clone the repository, for example:
 ```sh
 git clone https://github.com/artis-mcrt/artisatomic.git
+cd artistatomic
 ```
-Then from within the repository directory run:
+
+To use a uv project virtual environment with locked dependency versions run:
 ```sh
-python3 -m pip install -e .
+uv sync --frozen
+source .venv/bin/activate
+uv pip install -e .[dev]
 ```
 
-Tip: if you get an error on macOS >= 11 when installing the dependency 'tables', first run brew install hdf5 c-blosc
+Or to install into the system environment with pip:
+```sh
+python3 -m pip install -e .[dev]
+```
 
 ## Usage
-Run "makeartisatomicfiles" at the command-line to create adata.txt, compositiondata.txt, phixsdata_v2.txt, and transitiondata.txt. This code is not user friendly at all are requires manual editing of the Python scripts to change ions and data sources.
+Run "makeartisatomicfiles" at the command-line to create adata.txt, compositiondata.txt, phixsdata_v2.txt, and transitiondata.txt. This code is not user friendly and requires manual editing of the Python scripts to change ions and data sources.
 
 [![Build and test](https://github.com/artis-mcrt/artisatomic/actions/workflows/pythonapp.yml/badge.svg)](https://github.com/artis-mcrt/artisatomic/actions/workflows/pythonapp.yml)

pyproject.toml

@@ -23,9 +23,29 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 license = { text = "MIT" }
-dynamic = ["version", "dependencies"]
+dynamic = ["version"]
 requires-python = ">=3.10"
 readme = { file = "README.md", content-type = 'text/markdown' }
+dependencies = [
+    "argcomplete>=3.5.1",
+    "chiantipy>=0.15.1",
+    "h5py>=3.10.0",
+    "numpy>=1.26.1",
+    "pandas>=2.2.3",
+    "polars>=1.12.0",
+    "pyarrow>=18.1.0",
+    "scipy>=1.11.3",
+    "xopen[zstd]>=2.0.2",
+]
+
+[project.optional-dependencies]
+dev = [
+    "mypy>=1.13.0",
+    "pre-commit>=4.0.1",
+    "pytest>=8.3.3",
+    "ruff>=0.8.3",
+    "types-requests>=2.32.0.20241016",
+]
 
 [project.urls]
 Repository = "https://www.github.com/artis-mcrt/artisatomic"
@@ -159,9 +179,6 @@ where = ["."]
 include = ["*", "**/matplotlibrc", "**/data"]
 exclude = ["tests", "**/dist", "**/lib", "**/build", "*.egg-info", "**/.*"]
 
-[tool.setuptools.dynamic]
-dependencies = { file = ["requirements.txt"] }
-
 [tool.setuptools_scm]
 write_to = "_version.py"
 local_scheme = "no-local-version"