Move to uv

.github/workflows/python.yml

@@ -22,13 +22,13 @@ jobs:
         python-version: "3.11"
     - name: Install dependencies
       run: |
-        pip install poetry
-        poetry install
+        pip install uv
+        uv sync
     - name: Lint with ruff
-      run: poetry run ruff check
+      run: uv run ruff check
     - name: Check formatting with ruff
-      run: poetry run ruff format --check
+      run: uv run ruff format --check
     - name: Typecheck with mypy
-      run: poetry run mypy --strict src
+      run: uv run mypy --strict src
     - name: Test with pytest
-      run: poetry run pytest tests
+      run: uv run pytest tests

README.md

@@ -12,8 +12,8 @@ The `config` file is a file that is sourced in other bash scripts, and so must
 follow bash syntax. It describes which sources to install where.
 
 The install procedure is done through the following commands:
-1. Create a python virtual environment (e.g. `python -m venv /path/to/venv`) and source it (`source /path/to/venv/bin/activate`)
-2. Run `pip install .` in root folder. The cli tool `deploy` has been installed (`deploy --help` for information)
+1. Install [uv](https://docs.astral.sh/uv/getting-started/installation/): the package manager that we use
+2. Run `uv sync` in root folder. The cli tool `deploy` has been installed (`deploy --help` for information)
 3. Run `deploy build` in order to start the build process.
 
 # Development Using Docker

deploy_tests/test_pflotran.py

@@ -20,9 +20,9 @@ def test_version() -> None:
     )
 
     match = re.search(r" Pflotran (\d+\.\d+sv\d+)\+\n", proc.stdout.decode())
-    assert (
-        match
-    ), f"Version not found in the following pflotran output: {proc.stdout.decode()}"
+    assert match, (
+        f"Version not found in the following pflotran output: {proc.stdout.decode()}"
+    )
 
     # Get the version as set by `deploy test`
     version = semver.Version.parse(os.environ["pflotran_version"])

devenv.lock

@@ -3,10 +3,10 @@
     "devenv": {
       "locked": {
         "dir": "src/modules",
-        "lastModified": 1735883199,
+        "lastModified": 1772143911,
         "owner": "cachix",
         "repo": "devenv",
-        "rev": "d67d04ae2dd3bc3723e615003034ba752e8db8c3",
+        "rev": "83c4b5682b84fe04c049970792f38d5879d3c0f1",
         "type": "github"
       },
       "original": {
@@ -19,30 +19,51 @@
     "flake-compat": {
       "flake": false,
       "locked": {
-        "lastModified": 1733328505,
-        "owner": "edolstra",
+        "lastModified": 1767039857,
+        "owner": "NixOS",
         "repo": "flake-compat",
-        "rev": "ff81ac966bb2cae68946d5ed5fc4994f96d0ffec",
+        "rev": "5edf11c44bc78a0d334f6334cdaf7d60d732daab",
         "type": "github"
       },
       "original": {
-        "owner": "edolstra",
+        "owner": "NixOS",
         "repo": "flake-compat",
         "type": "github"
       }
     },
+    "git-hooks": {
+      "inputs": {
+        "flake-compat": "flake-compat",
+        "gitignore": "gitignore",
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1772024342,
+        "owner": "cachix",
+        "repo": "git-hooks.nix",
+        "rev": "6e34e97ed9788b17796ee43ccdbaf871a5c2b476",
+        "type": "github"
+      },
+      "original": {
+        "owner": "cachix",
+        "repo": "git-hooks.nix",
+        "type": "github"
+      }
+    },
     "gitignore": {
       "inputs": {
         "nixpkgs": [
-          "pre-commit-hooks",
+          "git-hooks",
           "nixpkgs"
         ]
       },
       "locked": {
-        "lastModified": 1709087332,
+        "lastModified": 1762808025,
         "owner": "hercules-ci",
         "repo": "gitignore.nix",
-        "rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
+        "rev": "cb5e3fdca1de58ccbc3ef53de65bd372b48f567c",
         "type": "github"
       },
       "original": {
@@ -52,11 +73,14 @@
       }
     },
     "nixpkgs": {
+      "inputs": {
+        "nixpkgs-src": "nixpkgs-src"
+      },
       "locked": {
-        "lastModified": 1733477122,
+        "lastModified": 1770434727,
         "owner": "cachix",
         "repo": "devenv-nixpkgs",
-        "rev": "7bd9e84d0452f6d2e63b6e6da29fe73fac951857",
+        "rev": "8430f16a39c27bdeef236f1eeb56f0b51b33d348",
         "type": "github"
       },
       "original": {
@@ -66,32 +90,31 @@
         "type": "github"
       }
     },
-    "pre-commit-hooks": {
-      "inputs": {
-        "flake-compat": "flake-compat",
-        "gitignore": "gitignore",
-        "nixpkgs": [
-          "nixpkgs"
-        ]
-      },
+    "nixpkgs-src": {
+      "flake": false,
       "locked": {
-        "lastModified": 1735882644,
-        "owner": "cachix",
-        "repo": "pre-commit-hooks.nix",
-        "rev": "a5a961387e75ae44cc20f0a57ae463da5e959656",
+        "lastModified": 1769922788,
+        "narHash": "sha256-H3AfG4ObMDTkTJYkd8cz1/RbY9LatN5Mk4UF48VuSXc=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "207d15f1a6603226e1e223dc79ac29c7846da32e",
         "type": "github"
       },
       "original": {
-        "owner": "cachix",
-        "repo": "pre-commit-hooks.nix",
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
         "type": "github"
       }
     },
     "root": {
       "inputs": {
         "devenv": "devenv",
+        "git-hooks": "git-hooks",
         "nixpkgs": "nixpkgs",
-        "pre-commit-hooks": "pre-commit-hooks"
+        "pre-commit-hooks": [
+          "git-hooks"
+        ]
       }
     }
   },

devenv.nix

@@ -1,19 +1,11 @@
-{ pkgs, lib, config, inputs, ... }:
+{
+  ...
+}:
 
 {
   languages.python = {
     enable = true;
-    package = pkgs.python311;
-    poetry.enable = true;
-    poetry.install.enable = true;
+    uv.enable = true;
+    venv.enable = true;
   };
-
-  # Build requirements
-  packages = with pkgs; [
-    autoconf
-    automake
-    libtool
-    gfortran
-    m4
-  ];
 }