TODO labeling; some noexcepts; test_todos_annoteted.py; test-time-requirements.txt

Author: slayoo

.github/workflows/conda.yml

@@ -25,11 +25,11 @@ jobs:
       - name: Install dependencies with pip in conda
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
+          pip install -r test-time-requirements.txt
       - name: Install PyPartMC
         run: |
           pip install -e .
       - name: Test with pytest
         run: |
           cd tests
-          pytest -v -s -We -p no:unraisableexception .
+          pytest -v -s -We -p no:unraisableexception -k 'not test_todos_annotated' .

.github/workflows/pdoc.yml

@@ -24,7 +24,7 @@ jobs:
         run: |
           pip install pdoc3
           pip install -e .
-          # TODO: add -We
+          # FIXME #23: add -We
           python -m pdoc --html PyPartMC
       - name: Deploy
         if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}

.github/workflows/pylint.yml

@@ -20,6 +20,7 @@ jobs:
         python-version: 3.9
     - run: |
         python -m pip install --upgrade pip
-        pip install pylint pytest nbconvert
+        pip install pylint
+        pip install -r test-time-requirements.txt
         pip install -e .
     - run: pylint --unsafe-load-any-extension=y --disable=fixme,no-member,trailing-newlines,missing-module-docstring,missing-class-docstring,missing-function-docstring,unnecessary-pass $(git ls-files '*.py')

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

@@ -15,10 +15,22 @@ on:
     types: [published]
 
 jobs:
+  todos_annotated:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          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
+
   build:
+    needs: [todos_annotated]
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-11, macOS-12, windows-latest]
+        platform: [ubuntu-latest, macos-11, macos-12, windows-latest]
         python-version: ["3.7", "3.8", "3.9", "3.10"]
     runs-on: ${{ matrix.platform }}
     steps:
@@ -54,7 +66,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - run: pip install pytest build wheel
+      - run: pip install build wheel
+      - run: pip install -r test-time-requirements.txt
 
       - run: |
           python -m build 2>&1 | tee build.log
@@ -81,7 +94,7 @@ jobs:
           name: dist
           path: dist
 
-      # TODO: should be doable on any OS
+      # TODO #114: should be doable on any OS
       - if: matrix.platform == 'windows-latest' || matrix.platform == 'ubuntu-latest'
         run: |
           pip install dist/*.whl
@@ -94,10 +107,10 @@ jobs:
       ### make sure PyPartMC is not picked up from a local folder
       - run: |
           cd tests
-          python -v -c "import PyPartMC"
-          pytest -v -s -We -p no:unraisableexception .
+          python -c "import PyPartMC"
+          pytest -v -s -We -p no:unraisableexception -k 'not test_todos_annotated' .
 
-# TODO: worth checking but perhaps in a separater workflow? (here conflicts with build dir created for manylinux by other user)
+# TODO #114: worth checking but perhaps in a separater workflow? (here conflicts with build dir created for manylinux by other user)
 #      - run: DEBUG=1 VERBOSE=1 pip install --verbose -e .
 #
 #      - run: pytest -v -s -We -p no:unraisableexception tests

CMakeLists.txt

@@ -13,11 +13,6 @@ set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED YES)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-# TODO
-#set(CMAKE_Fortran_STANDARD 2008)
-#set(CMAKE_Fortran_STANDARD_REQUIRED YES)
-#set(CMAKE_Fortran_EXTENSIONS OFF)
-
 if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
   add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-fimplicit-none>)
 endif()
@@ -84,7 +79,7 @@ function(scoped_sundials_setup_config)
   set(PROJECT_SOURCE_DIR ${SUNDIALS_SOURCE_DIR})
   set(SUNDIALS_PRECISION "double")
   set(SUNDIALS_CINDEX_TYPE "int64_t")
-  # TODO: read from submodule files!
+  # TODO #111: read from submodule files!
   set(PACKAGE_VERSION_MAJOR "5")
   set(PACKAGE_VERSION_MINOR "8")
   set(PACKAGE_VERSION_PATCH "0")
@@ -143,18 +138,11 @@ endif()
 
 ### pedantics ######################################################################################
 
-foreach(target _PyPartMC)  # TODO: the same for partmclib
+foreach(target _PyPartMC)
   target_compile_options(${target} PRIVATE
     $<$<CXX_COMPILER_ID:MSVC>:/W4 /WX>
     $<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wall -Wextra -Wpedantic -Werror>
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-compare-reals> # TODO
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-unused-dummy-argument> # TODO
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-unused-variable>  # TODO
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-c-binding-type>  # TODO
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-maybe-uninitialized> # TODO
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-function-elimination> # TODO
-    $<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-unused-parameter> # TODO
-    #$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-surprising> # TODO
+    $<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-unused-parameter> 
   )
 endforeach()
 

PyPartMC/__init__.py

@@ -22,7 +22,7 @@ def __build_extension_env():
         for cookie in cookies:
             cookie.close()
 
-# TODO: 2 x loop over prefixes and units
+# TODO #113: 2 x loop over prefixes and units
 si = namedtuple("SI", (
     "m", "cm", "um",
     "kg", "g",
@@ -38,7 +38,7 @@ def __build_extension_env():
     Pa=1., hPa=100.,
     mol=1.
 )
-""" TODO """
+""" TODO #113 """
 
 with __build_extension_env():
     from _PyPartMC import *

src/aero_data.hpp

@@ -22,7 +22,7 @@ struct AeroData {
     {
         gimmick_ptr() = std::make_unique<InputGimmick>(json);
         f_aero_data_from_json(this->ptr.f_arg());
-        gimmick_ptr().reset(); // TODO: guard
+        gimmick_ptr().reset(); // TODO #117: guard
     }
 
     static int spec_by_name(const AeroData &self, const std::string &name) {

src/aero_state.F90

@@ -41,8 +41,8 @@ subroutine f_aero_state_init(ptr_c, n_part, aero_data_ptr_c) bind(C)
     call aero_state_set_n_part_ideal(ptr_f, n_part)
     !call aero_state_add_aero_dist_sample(aero_state, aero_data_ptr_f, &
     !       aero_dist_init, 1d0, 0d0, &
-    !       .false. & ! TODO run_part_opt%allow_doubling, &
-    !       .false. & ! TODO run_part_opt%allow_halving)
+    !       .false. & ! TODO #121 run_part_opt%allow_doubling, &
+    !       .false. & ! TODO #121 run_part_opt%allow_halving)
     !)
 
   end subroutine

src/env_state.hpp

@@ -19,7 +19,7 @@ struct EnvState {
     EnvState(const nlohmann::json &json) :
         ptr(f_env_state_ctor, f_env_state_dtor)
     {
-        gimmick_ptr() = std::make_unique<InputGimmick>(json); // TODO: guard
+        gimmick_ptr() = std::make_unique<InputGimmick>(json); // TODO #117: guard
         f_env_state_from_json(this->ptr.f_arg());
         gimmick_ptr().reset();
     }

src/fake_mpi.F90

@@ -20,10 +20,11 @@ module mpi
     MPI_MAX = -1, &
     MPI_SUM = -1, &
     MPI_SUCCESS = -1, &
-    MPI_TAG = 1, &  ! TODO this is used as status array index
     MPI_ANY_TAG = -1, &
-    MPI_SOURCE = 1, & ! TODO this is used as status array index
-    MPI_ANY_SOURCE = -1
+    MPI_ANY_SOURCE = -1, &
+    ! status array indices
+    MPI_TAG = 1, &
+    MPI_SOURCE = 1 
 
   interface
     subroutine mpi_abort(comm, errorcode, ierror) bind(C)