Merge branch 'main' into gas_improvements

Conflicts:
	tests/test_gas_state.py

Author: jcurtis2

.github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit-hooks
+
+on: [pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.10"
+      - name: Linting
+        run: |
+          pip install pre-commit
+          pre-commit clean
+          pre-commit autoupdate
+          pre-commit run --all-files

.github/workflows/tests+artifacts+pypi.yml

@@ -24,21 +24,16 @@ jobs:
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
       - run: pip install -r test-time-requirements.txt
       - run: DEBUG=0 VERBOSE=1 pip install --verbose -e .
-      - run: pytest -v -s -We -p no:unraisableexception tests/test_todos_annotated.py
+      - env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: pytest -v -s -We -p no:unraisableexception tests/test_todos_annotated.py
 
   build:
     needs: [todos_annotated]
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-12, windows-latest]
         python-version: ["3.7", "3.8", "3.9", "3.10"]
-        exclude:
-          - platform: macos-12
-            python-version: "3.7"
-          - platform: macos-12
-            python-version: "3.8"
-          - platform: macos-12
-            python-version: "3.9"
     runs-on: ${{ matrix.platform }}
     steps:
       - if: startsWith(matrix.platform, 'macos-')
@@ -78,6 +73,7 @@ jobs:
       - run: pip install -r test-time-requirements.txt
 
       - run: |
+          unset CI
           python -m build 2>&1 | tee build.log
           exit `fgrep -i warning build.log | wc -l`
 

.gitmodules

@@ -4,7 +4,7 @@
 	shallow = true
 [submodule "partmc"]
 	path = gitmodules/partmc
-	url = https://github.com/compdyn/partmc
+	url = https://github.com/slayoo/partmc
 	shallow = true
 [submodule "pybind11_json"]
 	path = gitmodules/pybind11_json

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+files: '.py'
+exclude: '.git'
+default_stages: [commit]
+
+repos:
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: debug-statements

CMakeLists.txt

@@ -36,7 +36,7 @@ add_definitions("-DSUNDIALS_INT64_T=1")
 ### sources ########################################################################################
 
 set(PyPartMC_sources 
-  pypartmc.cpp gimmicks.cpp fake_netcdf.cpp fake_mpi.cpp fake_spec_file.cpp
+  pypartmc.cpp gimmicks.cpp fake_netcdf.cpp fake_spec_file.cpp sys.cpp
   run_part.F90 run_part_opt.F90 util.F90 aero_data.F90 aero_state.F90 env_state.F90 gas_data.F90 
   gas_state.F90 scenario.F90 condense.F90 aero_particle.F90 bin_grid.F90
   camp_core.F90 photolysis.F90
@@ -136,7 +136,7 @@ set(partmclib_SOURCES condense_solver.c aero_state.F90 integer_varray.F90 intege
   photolysis.F90
 )
 add_prefix(gitmodules/partmc/src/ partmclib_SOURCES)
-list(APPEND partmclib_SOURCES src/fake_mpi.F90 src/fake_netcdf.F90 src/fake_spec_file.F90)
+list(APPEND partmclib_SOURCES src/fake_netcdf.F90 src/fake_spec_file.F90 src/sys.F90)
 
 set(klu_SOURCES
   KLU/Source/klu_analyze.c
@@ -271,7 +271,6 @@ target_include_directories(camplib PRIVATE
 
 add_library(partmclib STATIC ${partmclib_SOURCES})
 target_compile_definitions(partmclib PRIVATE PMC_USE_SUNDIALS="1")
-target_compile_definitions(partmclib PRIVATE PMC_USE_MPI="1")
 target_compile_definitions(partmclib PRIVATE PMC_USE_CAMP="1")
 add_dependencies(partmclib ${SUNDIALS_items})
 target_include_directories(partmclib PRIVATE 
@@ -297,6 +296,9 @@ target_compile_definitions(_PyPartMC PRIVATE VERSION_INFO=${VERSION_INFO})
 target_link_libraries(_PyPartMC PRIVATE partmclib)
 if (APPLE)
   target_link_options(_PyPartMC PRIVATE -Wl,-no_compact_unwind -Wl,-keep_dwarf_unwind)
+  if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
+    target_link_libraries(_PyPartMC PRIVATE -static gfortran -dynamic)
+  endif()
 endif()
 if (WIN32)
   target_link_libraries(_PyPartMC PRIVATE -static gcc stdc++ winpthread quadmath -dynamic)

PyPartMC/__init__.py

@@ -1,8 +1,9 @@
 # pylint: disable=invalid-name,wrong-import-position
 import os
+from collections import namedtuple
 from contextlib import contextmanager
 from pathlib import Path
-from collections import namedtuple
+
 
 # https://github.com/diegoferigo/cmake-build-extension/blob/master/src/cmake_build_extension/__init__.py
 @contextmanager
@@ -11,8 +12,8 @@ def __build_extension_env():
     # https://docs.python.org/3/whatsnew/3.8.html#bpo-36085-whatsnew
     if hasattr(os, "add_dll_directory"):
         basepath = os.path.dirname(os.path.abspath(__file__))
-        dllspath = os.path.join(basepath, '..')
-        os.environ['PATH'] = dllspath + os.pathsep + os.environ['PATH']
+        dllspath = os.path.join(basepath, "..")
+        os.environ["PATH"] = dllspath + os.pathsep + os.environ["PATH"]
         for path in os.environ.get("PATH", "").split(os.pathsep):
             if path and Path(path).is_absolute() and Path(path).is_dir():
                 cookies.append(os.add_dll_directory(path))
@@ -22,25 +23,24 @@ def __build_extension_env():
         for cookie in cookies:
             cookie.close()
 
+
 # TODO #113: 2 x loop over prefixes and units
-si = namedtuple("SI", (
-    "m", "cm", "um", "nm",
-    "kg", "g",
-    "s",
-    "K",
-    "Pa", "hPa",
-    "mol"
-))(
-    m=1., cm=.01, um=1e-6, nm=1e-9,
-    kg=1., g=1e-3,
-    s=1.,
-    K=1.,
-    Pa=1., hPa=100.,
-    mol=1.
+si = namedtuple("SI", ("m", "cm", "um", "nm", "kg", "g", "s", "K", "Pa", "hPa", "mol"))(
+    m=1.0,
+    cm=0.01,
+    um=1e-6,
+    nm=1e-9,
+    kg=1.0,
+    g=1e-3,
+    s=1.0,
+    K=1.0,
+    Pa=1.0,
+    hPa=100.0,
+    mol=1.0,
 )
 """ TODO #113 """
 
 with __build_extension_env():
-    from _PyPartMC import *
-    from _PyPartMC import __all__, __version__
     import _PyPartMC
+    from _PyPartMC import *
+    from _PyPartMC import __all__, __version__  # pylint: disable=no-name-in-module

README.md

@@ -96,6 +96,7 @@ warning: no files found matching 'gitmodules/...
 ```
 Since git clone was done without recursive option, try: `git submodule update --init`
 
+## Notes for developers
 #### How to debug
 ```sh
 git clone --recursive git+https://github.com/open-atmos/PyPartMC.git
@@ -104,6 +105,8 @@ DEBUG=1 VERBOSE=1 pip --verbose install -e .
 gdb python 
 (gdb) run -m pytest -s -vv -We -p no:unraisableexception tests
 ```
+#### Pre-commit hooks
+PyPartMC codebase benefits from Pylint, Black and isort code analysis (which are all part of the CI workflows where we also use pre-commit hooks. The pre-commit hooks can be run locally, and then the resultant changes need to be staged before committing. To set up the hooks locally, install pre-commit via `pip install pre-commit` and set up the git hooks via `pre-commit install` (this needs to be done every time you clone the project). To run all pre-commit hooks, run `pre-commit run --all-files`. The `.pre-commit-config.yaml` file can be modified in case new hooks are to be added or existing ones need to be altered.
 
 ## Credits
 

gitmodules/partmc

@@ -9,7 +9,8 @@
 import subprocess
 import sys
 from pathlib import Path
-from setuptools import Extension, setup, find_packages
+
+from setuptools import Extension, find_packages, setup
 from setuptools.command.build_ext import build_ext
 
 # Convert distutils Windows platform specifiers to CMake -A arguments
@@ -140,11 +141,11 @@ def build_extension(self, ext):  # pylint: disable=too-many-branches
     zip_safe=False,
     python_requires=">=3.7",
     setup_requires=["setuptools_scm"],
-    install_requires=['numpy'],
+    install_requires=["numpy"],
     license="GPL-3.0",
     project_urls={
         "Tracker": "https://github.com/open-atmos/PyPartMC/issues",
         "Documentation": "https://open-atmos.github.io/PyPartMC",
         "Source": "https://github.com/open-atmos/PyPartMC/",
-    }
+    },
 )

setup.py

@@ -16,6 +16,7 @@ subroutine f_aero_data_ctor(ptr_c) bind(C)
     type(c_ptr), intent(out) :: ptr_c
 
     allocate(ptr_f)
+    call fractal_set_spherical(ptr_f%fractal)
     ptr_c = c_loc(ptr_f)
   end subroutine