Merge branch 'develop' of https://github.com/stan-dev/cmdstanpy into develop

Author: mitzimorris

.github/workflows/main.yml

@@ -13,7 +13,7 @@ on:
       cmdstan-version:
         description: 'Version to test'
         required: false
-        default: 'latest'
+        default: ''
 
 jobs:
   get-cmdstan-version:
@@ -24,7 +24,7 @@ jobs:
       - name: Get CmdStan version
         id: check-cmdstan
         run: |
-            if [[ "${{ github.event.inputs.cmdstan-version }}" == "latest" ]]; then
+            if [[ "${{ github.event.inputs.cmdstan-version }}" != "" ]]; then
               echo "::set-output name=version::${{ github.event.inputs.cmdstan-version }}"
             else
                 echo "::set-output name=version::$(python -c 'import requests;print(requests.get("https://api.github.com/repos/stan-dev/cmdstan/releases/latest").json()["tag_name"][1:])')"
@@ -96,14 +96,14 @@ jobs:
         run: |
           install_cmdstan -h
           install_cxx_toolchain -h
-          python -m cmdstanpy.install_cmdstan
+          python -m cmdstanpy.install_cmdstan --version ${{ needs.get-cmdstan-version.outputs.version }}
 
       - name: Install CmdStan (Windows)
         if: matrix.os == 'windows-latest'
         run: |
           install_cmdstan -h
           install_cxx_toolchain -h
-          python -m cmdstanpy.install_cmdstan --compiler
+          python -m cmdstanpy.install_cmdstan --compiler --version ${{ needs.get-cmdstan-version.outputs.version }}
 
       - name: Run tests
         run: |

cmdstanpy/model.py

@@ -161,12 +161,12 @@ def __init__(
                     self._compiler_options.add_include_path(path)
 
             # try to detect models w/out parameters, needed for sampler
-            if not cmdstan_version_before(2, 27) and cmdstan_version_before(
-                2, 29
-            ):
+            if not cmdstan_version_before(
+                2, 27
+            ):  # unknown end of version range
                 model_info = self.src_info()
                 if 'parameters' in model_info:
-                    self._fixed_param = len(model_info['parameters']) == 0
+                    self._fixed_param |= len(model_info['parameters']) == 0
 
         if exe_file is not None:
             self._exe_file = os.path.realpath(os.path.expanduser(exe_file))
@@ -275,19 +275,25 @@ def src_info(self) -> Dict[str, Any]:
             return result
         try:
             cmd = (
-                [os.path.join('.', 'bin', 'stanc' + EXTENSION)]
+                [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
                 # handle include-paths, allow-undefined etc
                 + self._compiler_options.compose_stanc()
                 + [
                     '--info',
                     self.stan_file,
                 ]
             )
-            sout = io.StringIO()
-            do_command(cmd=cmd, cwd=cmdstan_path(), fd_out=sout)
-            result = json.loads(sout.getvalue())
+            proc = subprocess.run(
+                cmd, capture_output=True, text=True, check=True
+            )
+            result = json.loads(proc.stdout)
             return result
-        except (ValueError, RuntimeError) as e:
+        except (
+            ValueError,
+            RuntimeError,
+            OSError,
+            subprocess.CalledProcessError,
+        ) as e:
             get_logger().debug(e)
             return result
 

requirements.txt

@@ -1,4 +1,4 @@
 pandas
-numpy>=1.15,!=1.19.4
+numpy>=1.21
 ujson
 tqdm

test/conftest.py

@@ -1,5 +1,7 @@
 """The global configuration for the test suite"""
+import atexit
 import os
+import shutil
 import subprocess
 
 import pytest
@@ -13,7 +15,16 @@
 
 @pytest.fixture(scope='session', autouse=True)
 def cleanup_test_files():
+
+    import cmdstanpy
+
+    # see https://github.com/pytest-dev/pytest/issues/5502
+    atexit.unregister(cmdstanpy._cleanup_tmpdir)
+
     yield
+
+    shutil.rmtree(cmdstanpy._TMPDIR, ignore_errors=True)
+
     subprocess.Popen(
         ['git', 'clean', '-fX', DATAFILES_PATH],
         stdout=subprocess.DEVNULL,

test/test_sample.py

@@ -1157,17 +1157,18 @@ def test_diagnose_divergences(self):
         ]
         fit = CmdStanMCMC(runset)
         # TODO - use cmdstan test files instead
-        expected = '\n'.join(
-            [
-                'Checking sampler transitions treedepth.',
-                '424 of 1000 (42%) transitions hit the maximum '
-                'treedepth limit of 8, or 2^8 leapfrog steps.',
-                'Trajectories that are prematurely terminated '
-                'due to this limit will result in slow exploration.',
-                'For optimal performance, increase this limit.',
-            ]
-        )
-        self.assertIn(expected, fit.diagnose().replace('\r\n', '\n'))
+        expected = [
+            'Checking sampler transitions treedepth.',
+            '424 of 1000',
+            'treedepth limit of 8, or 2^8 leapfrog steps.',
+            'Trajectories that are prematurely terminated '
+            'due to this limit will result in slow exploration.',
+            'For optimal performance, increase this limit.',
+        ]
+
+        diagnose = fit.diagnose()
+        for e in expected:
+            self.assertIn(e, diagnose)
 
     def test_validate_bad_run(self):
         exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)