Merge pull request #101 from cropsinsilico/minor

Minor
cropsinsilico · Oct 12, 2023 · bc23d79 · bc23d79
2 parents 70ad737 + e4a5540
commit bc23d79
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diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml
@@ -432,13 +432,17 @@ jobs:
       run: python utils/setup_test_env.py verify
     - name: Compile libraries
       run: yggcompile
-    - if: runner.os == 'Windows'
-      name: Run cmake test in command prompt
-      run: 'cmake -h
-
-        pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
-
-        '
+    - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
+        == 'mamba')
+      name: Run cmake test in command prompt (CONDA)
+      run: conda activate test && pytest --import-mode=importlib --ci --cov-append
+        --nocapture tests/drivers/test_CMakeModelDriver.py
+      shell: cmd /C CALL {0}
+      timeout-minutes: 180
+    - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
+        != 'mamba'
+      name: Run cmake test in command prompt (PIP)
+      run: pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - continue-on-error: true
@@ -779,13 +783,17 @@ jobs:
       run: python utils/setup_test_env.py verify
     - name: Compile libraries
       run: yggcompile
-    - if: runner.os == 'Windows'
-      name: Run cmake test in command prompt
-      run: 'cmake -h
-
-        pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
-
-        '
+    - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
+        == 'mamba')
+      name: Run cmake test in command prompt (CONDA)
+      run: conda activate test && pytest --import-mode=importlib --ci --cov-append
+        --nocapture tests/drivers/test_CMakeModelDriver.py
+      shell: cmd /C CALL {0}
+      timeout-minutes: 180
+    - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
+        != 'mamba'
+      name: Run cmake test in command prompt (PIP)
+      run: pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - continue-on-error: true
@@ -1118,13 +1126,17 @@ jobs:
       run: python utils/setup_test_env.py verify
     - name: Compile libraries
       run: yggcompile
-    - if: runner.os == 'Windows'
-      name: Run cmake test in command prompt
-      run: 'cmake -h
-
-        pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
-
-        '
+    - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
+        == 'mamba')
+      name: Run cmake test in command prompt (CONDA)
+      run: conda activate test && pytest --import-mode=importlib --ci --cov-append
+        --nocapture tests/drivers/test_CMakeModelDriver.py
+      shell: cmd /C CALL {0}
+      timeout-minutes: 180
+    - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
+        != 'mamba'
+      name: Run cmake test in command prompt (PIP)
+      run: pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - continue-on-error: true
@@ -1440,13 +1452,17 @@ jobs:
       run: python utils/setup_test_env.py verify
     - name: Compile libraries
       run: yggcompile
-    - if: runner.os == 'Windows'
-      name: Run cmake test in command prompt
-      run: 'cmake -h
-
-        pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
-
-        '
+    - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
+        == 'mamba')
+      name: Run cmake test in command prompt (CONDA)
+      run: conda activate test && pytest --import-mode=importlib --ci --cov-append
+        --nocapture tests/drivers/test_CMakeModelDriver.py
+      shell: cmd /C CALL {0}
+      timeout-minutes: 180
+    - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
+        != 'mamba'
+      name: Run cmake test in command prompt (PIP)
+      run: pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - continue-on-error: true
@@ -1761,13 +1777,17 @@ jobs:
       run: python utils/setup_test_env.py verify
     - name: Compile libraries
       run: yggcompile
-    - if: runner.os == 'Windows'
-      name: Run cmake test in command prompt
-      run: 'cmake -h
-
-        pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
-
-        '
+    - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
+        == 'mamba')
+      name: Run cmake test in command prompt (CONDA)
+      run: conda activate test && pytest --import-mode=importlib --ci --cov-append
+        --nocapture tests/drivers/test_CMakeModelDriver.py
+      shell: cmd /C CALL {0}
+      timeout-minutes: 180
+    - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
+        != 'mamba'
+      name: Run cmake test in command prompt (PIP)
+      run: pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - continue-on-error: true

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,13 @@
 History
 =======
 
+1.10.2 (2023-10-12) Minor bug fixes and dependency updates
+-------------------
+
+* Updated rapidjson version to include normalization of units in human readable strings
+* Fix CI R dependency installation bug by pinning vdiffr to 1.0.5
+* Fix bug in types test that assumed different directory structure
+
 1.10.1 (2023-06-27) New map transformation, composite function wrapping example, and various refactoring of internal methods
 -------------------
 

diff --git a/_vendor/python_rapidjson/units.cpp b/_vendor/python_rapidjson/units.cpp
@@ -1368,6 +1368,18 @@ static PyObject* quantity_array__array_ufunc__(PyObject* self, PyObject* args, P
 		    goto cleanup;
 		}
 	    }
+	} else if (ufunc_name == "exp") {
+	    if (_has_units(i0)) {
+		tmp2 = _get_units(i0);
+		if (((UnitsObject*)tmp2)->units->is_null()) {
+		    Py_DECREF(tmp2);
+		    convert_units = get_empty_units();
+		} else {
+		    // Allow radians here?
+		    Py_DECREF(tmp2);
+		    goto cleanup;
+		}
+	    }
 	} else if (ufunc_name == "sin" ||
 		   ufunc_name == "cos" ||
 		   ufunc_name == "tan" ||

diff --git a/docs/source/development/todo.rst b/docs/source/development/todo.rst
@@ -20,6 +20,7 @@ Documentation
 * Expand development section into contributing guide
 * Go through and update/prune interface documentation
 * Docs on default_file/default_value
+* Docs on use of YggInterface.h vs YggLibrary.h in main source vs. other source files when a module has more than one
 
 Refactor
 --------

diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "yggdrasil" %}
-{% set version = "1.10.1" %}
+{% set version = "1.10.2" %}
 {% set PY_VER_MAJOR = PY_VER.split('.')[0] %}
 {% set PY_VER_MINOR = PY_VER.split('.')[1] %}
 
@@ -122,6 +122,7 @@ outputs:
         - python
         - r-base
         - r-bit64
+        - r-devtools  # [not win]
         - r-r6
         - r-reticulate
         - r-units
@@ -130,6 +131,7 @@ outputs:
         - {{ pin_subpackage('yggdrasil', exact=True) }}
         - r-base
         - r-bit64
+        - r-devtools  # [not win]
         - r-r6
         - r-reticulate
         - r-units

diff --git a/tests/drivers/test_CompiledModelDriver.py b/tests/drivers/test_CompiledModelDriver.py
@@ -197,7 +197,7 @@ def test_get_flags(self, python_class):
         from yggdrasil import __version__ as yggver
         yggver = yggver.split('+')[0].split('v')[-1].split('.')
         assert (python_class.get_flags(flags='hello', libtype='object')
-                == ['hello', '-DWITH_YGGDRASIL',
+                == ['hello', '-DWITH_YGGDRASIL', '-D_USE_MATH_DEFINES',
                     f'-DYGGVER_MAJOR={yggver[0]}'])
 
     def test_get_executable_command(self, python_class):

diff --git a/tests/examples/types/types.py b/tests/examples/types/types.py
@@ -1,6 +1,6 @@
 import os
 import argparse
-from yggdrasil.examples.tests.test_types import TestExampleTypes
+from tests.examples.test_types import TestExampleTypes
 from yggdrasil.languages import get_language_ext
 from yggdrasil.runner import run
 _this_dir = os.path.dirname(__file__)

diff --git a/utils/requirements/requirements.json b/utils/requirements/requirements.json
@@ -218,6 +218,53 @@
             ]
           }
         },
+        {
+          "r-devtools": {
+            "options": [
+              {
+                "method": "conda",
+                "host": true,
+                "os": "unix"
+              },
+              {
+                "method": "cran"
+              },
+              {
+                "method": "skip",
+                "os": "win"
+              }
+            ]
+          }
+        },
+        {
+          "harfbuzz": {
+            "options": [
+              {
+                "name": "libharfbuzz-dev",
+                "method": "apt",
+                "add": [
+                  "libfribidi-dev",
+                  "r-cran-devtools"
+                ]
+              },
+              {
+                "name": "harfbuzz",
+                "add": [
+                  "fribidi",
+                  "libgit2"
+                ],
+                "method": "brew"
+              },
+              {
+                "method": "skip",
+                "os": "win"
+              },
+              {
+                "method": "conda_skip"
+              }
+            ]
+          }
+        },
         {
           "r-bit64": [
             {

diff --git a/utils/requirements/requirements.yaml b/utils/requirements/requirements.yaml
@@ -133,6 +133,25 @@ extras:
           add: [r-base-dev]
         - name: r
           method: brew
+    - r-devtools:
+        options:
+        - method: conda
+          host: True
+          os: unix
+        - method: cran
+        - method: skip
+          os: win
+    - harfbuzz:
+        options:
+        - name: libharfbuzz-dev
+          method: apt
+          add: [libfribidi-dev, r-cran-devtools]
+        - name: harfbuzz
+          add: [fribidi, libgit2]
+          method: brew
+        - method: skip
+          os: win
+        - method: conda_skip
     - r-bit64:
         - method: conda
           host: True

diff --git a/utils/requirements/requirements_condaonly.txt b/utils/requirements/requirements_condaonly.txt
@@ -15,6 +15,7 @@ msmpi; platform_system == 'Windows'  # [conda,mpi]
 openmpi; platform_system == 'Darwin'  # [conda,mpi]
 r-base           # [conda,r]
 r-bit64          # [conda,r]
+r-devtools; platform_system != 'Windows'  # [conda,r]
 r-r6             # [conda,r]
 r-reticulate     # [conda,r]
 r-units          # [conda,r]

diff --git a/utils/setup_test_env.py b/utils/setup_test_env.py
@@ -522,17 +522,24 @@ def add_argument(*a_args, **a_kwargs):
 
 
 def prune_windows_path():
-    to_remove = [
-        'C:\\Program Files\\Microsoft SQL Server\\140\\DTS\\Binn',
-        'C:\\Program Files\\Microsoft SQL Server\\150\\DTS\\Binn',
-        'C:\\Program Files\\Microsoft SQL Server\\160\\DTS\\Binn']
-    print(f"PRUNING PATH: {os.environ['PATH']}")
-    path_list = os.environ['PATH'].split(os.pathsep)
-    for x in to_remove:
-        if x in path_list:
-            path_list.remove(x)
+    to_remove = (
+        'C:\\Program Files\\Microsoft SQL Server', )
+    # to_remove = [
+    #     'C:\\Program Files\\Microsoft SQL Server\\140\\DTS\\Binn',
+    #     'C:\\Program Files\\Microsoft SQL Server\\150\\DTS\\Binn',
+    #     'C:\\Program Files\\Microsoft SQL Server\\160\\DTS\\Binn']
+    print(f"PRUNING PATH ({len(os.environ['PATH'])}): "
+          f"{os.environ['PATH']}")
+    old_path_list = os.environ['PATH'].split(os.pathsep)
+    path_list = []
+    for x in old_path_list:
+        if not x.startswith(to_remove):
+            path_list.append(x)
+    # for x in to_remove:
+    #     if x in path_list:
+    #         path_list.remove(x)
     new_path = os.pathsep.join(path_list)
-    print(f"PRUNED PATH: {new_path}")
+    print(f"PRUNED PATH ({len(os.environ['PATH'])}): {new_path}")
     cmds = [f"set \"PATH={new_path}\""]
     return cmds
 

diff --git a/utils/test-install-base.yml b/utils/test-install-base.yml
@@ -263,14 +263,18 @@ jobs:
       run: python utils/setup_test_env.py verify
     - name: Compile libraries
       run: yggcompile
-    - name: Run cmake test in command prompt
+    - name: Run cmake test in command prompt (CONDA)
       timeout-minutes: 180
-      if: runner.os == 'Windows'
+      if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method == 'mamba')
       shell: cmd /C CALL {0}
-      run: |
-        cmake -h
+      run: >-
+        conda activate test && pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
+    - name: Run cmake test in command prompt (PIP)
+      timeout-minutes: 180
+      if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method != 'mamba'
+      shell: cmd /C CALL {0}
+      run: >-
         pytest --import-mode=importlib --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
-
     - name: Run tests (1st)
       timeout-minutes: 180
       id: test1

diff --git a/yggdrasil/drivers/CModelDriver.py b/yggdrasil/drivers/CModelDriver.py
@@ -554,11 +554,13 @@ class MSVCArchiver(ArchiverBase):
         libtype_order = ['static', 'shared']
     else:
         libtype_order = ['shared', 'static']
-    _python_lib = ygg_cfg.get('c', 'python_%s' % libtype_order[0],
-                              ygg_cfg.get('c', 'python_%s' % libtype_order[1], None))
-    if (_python_lib is None) or (not os.path.isfile(_python_lib)):  # pragma: no cover
-        _python_lib = tools.get_python_c_library(
-            allow_failure=True, libtype=libtype_order[0])
+    _python_lib = ygg_cfg.get('c', f'python_{libtype_order[0]}',
+                              ygg_cfg.get('c', f'python_{libtype_order[1]}', None))
+    for _python_libtype in libtype_order:
+        if (_python_lib is not None) and os.path.isfile(_python_lib):
+            break
+        _python_lib = tools.get_python_c_library(  # pragma: no cover
+            allow_failure=True, libtype=_python_libtype)
 except BaseException as e:  # pragma: debug
     warnings.warn("ERROR LOCATING PYTHON LIBRARY: %s" % e)
     _python_lib = None

diff --git a/yggdrasil/drivers/CompiledModelDriver.py b/yggdrasil/drivers/CompiledModelDriver.py
@@ -1592,6 +1592,7 @@ def get_flags(cls, dont_link=None, add_linker_switch=False,
             from yggdrasil import __version__
             kwargs.setdefault('definitions', [])
             kwargs['definitions'].append('WITH_YGGDRASIL')
+            kwargs['definitions'].append('_USE_MATH_DEFINES')
             yggver = __version__.split('+')[0].split('v')[-1].split('.')
             if len(yggver) > 0:
                 kwargs['definitions'] += [f'YGGVER_MAJOR={yggver[0]}']