python310Packages.cmdstanpy: init at 1.1.0

2023-07-18 17:06:35 +02:00
parent a5ca6a0f2e
commit 4df9ed01d3
3 changed files with 109 additions and 0 deletions
@@ -0,0 +1,82 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, substituteAll
+
+, cmdstan
+
+, pandas
+, numpy
+, tqdm
+, xarray
+
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "cmdstanpy";
+  version = "1.1.0";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "stan-dev";
+    repo = "cmdstanpy";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-9kAd3rbSctWEhAzB6RiQlbg5/uVxGIghYLus8hWzBFQ=";
+  };
+
+  patches = [
+    (substituteAll {
+      src = ./use-nix-cmdstan-path.patch;
+      cmdstan = "${cmdstan}/opt/cmdstan";
+    })
+  ];
+
+  postPatch = ''
+    # conftest.py would have used git to clean up, which is unnecessary here
+    rm test/conftest.py
+  '';
+
+  propagatedBuildInputs = [
+    pandas
+    numpy
+    tqdm
+  ];
+
+  passthru.optional-dependencies = {
+    all = [ xarray ];
+  };
+
+  preCheck = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ] ++ passthru.optional-dependencies.all;
+
+  disabledTestPaths = [
+    # No need to test these when using Nix
+    "test/test_install_cmdstan.py"
+    "test/test_cxx_installation.py"
+  ];
+
+  disabledTests = [
+    "test_lp_good" # Fails for some reason
+    "test_serialization" # Pickle class mismatch errors
+    # These tests use the flag -DSTAN_THREADS which doesn't work in cmdstan (missing file)
+    "test_multi_proc_threads"
+    "test_compile_force"
+  ];
+
+  pythonImportsCheck = [ "cmdstanpy" ];
+
+  meta = {
+    homepage = "https://github.com/stan-dev/cmdstanpy";
+    description = "A lightweight interface to Stan for Python users";
+    changelog = "https://github.com/stan-dev/cmdstanpy/releases/tag/v${version}";
+    license = lib.licenses.bsd3;
+    platforms = lib.platforms.linux;
+    maintainers = with lib.maintainers; [ tomasajt ];
+  };
+}
@@ -0,0 +1,25 @@
+diff --git a/cmdstanpy/utils/cmdstan.py b/cmdstanpy/utils/cmdstan.py
+index 227d97a..27c3ccc 100644
+--- a/cmdstanpy/utils/cmdstan.py
+++ b/cmdstanpy/utils/cmdstan.py
+@@ -163,19 +163,7 @@ def cmdstan_path() -> str:
+     if 'CMDSTAN' in os.environ and len(os.environ['CMDSTAN']) > 0:
+         cmdstan = os.environ['CMDSTAN']
+     else:
+-        cmdstan_dir = os.path.expanduser(os.path.join('~', _DOT_CMDSTAN))
+-        if not os.path.exists(cmdstan_dir):
+-            raise ValueError(
+-                'No CmdStan installation found, run command "install_cmdstan"'
+-                'or (re)activate your conda environment!'
+-            )
+-        latest_cmdstan = get_latest_cmdstan(cmdstan_dir)
+-        if latest_cmdstan is None:
+-            raise ValueError(
+-                'No CmdStan installation found, run command "install_cmdstan"'
+-                'or (re)activate your conda environment!'
+-            )
+-        cmdstan = os.path.join(cmdstan_dir, latest_cmdstan)
+        cmdstan = '@cmdstan@'
+         os.environ['CMDSTAN'] = cmdstan
+     validate_cmdstan_path(cmdstan)
+     return os.path.normpath(cmdstan)
@@ -2001,6 +2001,8 @@ self: super: with self; {

  cmdline = callPackage ../development/python-modules/cmdline { };

+  cmdstanpy = callPackage ../development/python-modules/cmdstanpy { };
+
  cmigemo = callPackage ../development/python-modules/cmigemo {
    inherit (pkgs) cmigemo;
  };