build: migrate nix build files from nix-extra

docs_src/marimo/validation.py → marimos/validation.py

@@ -16,11 +16,11 @@ def _():
     from pathlib import Path
 
     import geopandas as gpd
+    import marimo as mo
     import pyogrio
 
     import fractopo.general
     import fractopo.tval.trace_validation
-    import marimo as mo
 
     return BytesIO, Path, fractopo, gpd, logging, mo, pyogrio
 

nix/package.nix

@@ -0,0 +1,112 @@
+{ buildPythonPackage, lib, click, pytest, geopandas, joblib, matplotlib, numpy
+, pandas, rich, scikit-learn, scipy, seaborn, shapely, typer, pytest-regressions
+, hypothesis, poetry-core, sphinxHook, pandoc, sphinx-autodoc-typehints
+, sphinx-rtd-theme, sphinx-gallery, nbsphinx, notebook, ipython, coverage
+, powerlaw, python-ternary, marimo,
+
+}:
+
+let
+
+  baseFiles =
+    [ ../pyproject.toml ../fractopo ../README.rst ../tests ../marimos ];
+  docFiles = baseFiles ++ [ ../docs_src ../examples ];
+  mkSrc = files:
+    let
+      fs = lib.fileset;
+      sourceFiles = fs.intersection (fs.gitTracked ../.) (fs.unions files);
+      src = fs.toSource {
+        root = ../.;
+        fileset = sourceFiles;
+      };
+    in src;
+  self = buildPythonPackage {
+    pname = "fractopo";
+    version = "0.7.0";
+
+    src = mkSrc baseFiles;
+
+    # TODO: Conflicts when other package also includes the same file
+    # nix puts both in site-packages/ directory
+    # postPatch = ''
+    #   substituteInPlace pyproject.toml \
+    #       --replace-fail 'include = ["CHANGELOG.md"]' ""
+    # '';
+    format = "pyproject";
+
+    nativeBuildInputs = [
+      # Uses poetry for install
+      poetry-core
+    ];
+
+    passthru = {
+      # Enables building package without tests
+      # nix build .#fractopo.passthru.no-check
+      no-check = self.overridePythonAttrs (_: { doCheck = false; });
+      # Documentation without tests
+      documentation = self.overridePythonAttrs (prevAttrs: {
+        src = mkSrc docFiles;
+        doCheck = false;
+        nativeBuildInputs = prevAttrs.nativeBuildInputs ++ [
+          # Documentation dependencies
+          sphinxHook
+          pandoc
+          sphinx-autodoc-typehints
+          sphinx-rtd-theme
+          sphinx-gallery
+          nbsphinx
+          notebook
+          ipython
+        ];
+        sphinxRoot = "docs_src";
+        outputs = [ "out" "doc" ];
+      });
+    };
+
+    propagatedBuildInputs = [
+      click
+      geopandas
+      joblib
+      matplotlib
+      numpy
+      pandas
+      powerlaw
+      python-ternary
+      rich
+      scikit-learn
+      scipy
+      seaborn
+      shapely
+      typer
+    ];
+
+    checkInputs = [ pytest pytest-regressions hypothesis coverage marimo ];
+
+    # TODO: Should this be precheck or does postInstall affect the docs build as well?
+    postInstall = ''
+      HOME="$(mktemp -d)"
+      export HOME
+      FRACTOPO_DISABLE_CACHE="1"
+      export FRACTOPO_DISABLE_CACHE
+    '';
+
+    checkPhase = ''
+      runHook preCheck
+      python -m coverage run --source fractopo -m pytest --hypothesis-seed=1
+      runHook postCheck
+    '';
+
+    postCheck = ''
+      python -m coverage report --fail-under 70
+    '';
+
+    pythonImportsCheck = [ "fractopo" ];
+
+    meta = with lib; {
+      homepage = "https://github.com/nialov/fractopo";
+      description = "Fracture Network analysis";
+      license = licenses.mit;
+      maintainers = [ maintainers.nialov ];
+    };
+  };
+in self

per-system.nix

@@ -1,4 +1,4 @@
-({ self, inputs, ... }:
+({ inputs, ... }:
 
   {
     perSystem = { self', config, system, pkgs, lib, ... }:
@@ -12,10 +12,10 @@
 
               (final: prev: {
                 pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [
-                  (_: pythonPrev: {
-                    "fractopo" = pythonPrev.fractopo.overridePythonAttrs
-                      # Test with local source
-                      (_: { src = self.outPath; });
+                  (pythonFinal: _: {
+                    fractopo = pythonFinal.callPackage ./nix/package.nix {
+                      inherit inputs;
+                    };
                   })
                 ];
                 inherit (final.python3Packages) fractopo;

pyproject.toml

@@ -25,7 +25,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3 :: Only"
 ]
-include = ["CHANGELOG.md"]
+# include = ["CHANGELOG.md"]
 
 [tool.poetry.scripts]
 fractopo = "fractopo.__main__:APP"

tests/marimo/test_validation.py → tests/marimos/test_validation.py

@@ -8,7 +8,7 @@
 
 SAMPLE_DATA_DIR = Path(__file__).parent.parent.joinpath("sample_data/")
 VALIDATION_NOTEBOOK = Path(__file__).parent.parent.parent.joinpath(
-    "docs_src/marimo/validation.py"
+    "marimos/validation.py"
 )
 PYTHON_INTERPRETER = sys.executable