Merge pull request #163 from zdaq12/pre-commit

adding pre-commit hooks. closes #6

Author: slayoo

.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

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+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
+
+  - 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

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():
+    import _PyPartMC
     from _PyPartMC import *
     from _PyPartMC import __all__, __version__
-    import _PyPartMC

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
 

setup.py

@@ -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/",
-    }
+    },
 )

src/pypartmc.cpp

@@ -48,18 +48,18 @@ PYBIND11_MODULE(_PyPartMC, m) {
     py::class_<AeroData>(m, "AeroData",
         R"pbdoc(
              Aerosol material properties and associated data.
- 
+
              The data in this structure is constant, as it represents physical
              quantities that cannot change over time.
-   
+
              Each aerosol species is identified by an index <tt>i =
              1,...,aero_data_n_spec(aero_data)</tt>. Then \c name(i) is the name of
              that species, \c density(i) is its density, etc. The ordering of the
              species is arbitrary and should not be relied upon (currently it is the
              order in the species data file). The only exception is that it is
              possible to find out which species is water from the \c i_water
              variable.
-  
+
              The names of the aerosol species are not important to PartMC, as
              only the material properties are used. The names are used for
              input and output, and also for communication with MOSAIC. For the
@@ -86,7 +86,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
     py::class_<AeroParticle>(m, "AeroParticle",
         R"pbdoc(
              Single aerosol particle data structure.
-  
+
              The \c vol array stores the total volumes of the different
              species that make up the particle. This array must have length
              equal to aero_data%%n_spec, so that \c vol(i) is the volume (in
@@ -122,12 +122,12 @@ PYBIND11_MODULE(_PyPartMC, m) {
     py::class_<AeroState>(m, "AeroState",
         R"pbdoc(
              The current collection of aerosol particles.
-  
+
              The particles in \c aero_state_t are stored in a single flat
              array (the \c apa data member), with a sorting into size bins and
              weight groups/classes possibly stored in the \c aero_sorted data
              member (if \c valid_sort is true).
-  
+
              Every time we remove particles we keep track of the particle ID
              and the action performed in the aero_info_array_t structure. This
              is typically cleared each time we output data to disk.
@@ -160,7 +160,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
     py::class_<GasData>(m, "GasData",
         R"pbdoc(
             Constant gas data.
-    
+
             Each gas species is identified by an integer \c i between 1 and
             \c gas_data_n_spec(gas_data). Species \c i has name \c gas_data%%name(i).
             The variable gas data describing the current mixing ratios is stored
@@ -178,7 +178,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
         "EnvState",
         R"pbdoc(
             Current environment state.
-    
+
             All quantities are instantaneous, describing the state at a
             particular instant of time. Constant data and other data not
             associated with the current environment state is stored in
@@ -218,7 +218,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
         "Scenario",
         R"pbdoc(
             This is everything needed to drive the scenario being simulated.
-  
+
             The temperature, pressure, emissions and background states are profiles
             prescribed as functions of time by giving a number of times and
             the corresponding data. Simple data such as temperature and pressure is
@@ -244,11 +244,11 @@ PYBIND11_MODULE(_PyPartMC, m) {
         "GasState",
         R"pbdoc(
             Current state of the gas mixing ratios in the system.
-  
+
             The gas species are defined by the gas_data_t structure, so that
             \c gas_state%%mix_rat(i) is the current mixing ratio of the gas
             with name \c gas_data%%name(i), etc.
-    
+
             By convention, if gas_state_is_allocated() return \c .false.,
             then the gas_state is treated as zero for all operations on
             it. This will be the case for new \c gas_state_t structures.
@@ -265,7 +265,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
             "returns a string with JSON representation of the object")
     ;
 
-    py::class_<RunPartOpt>(m, 
+    py::class_<RunPartOpt>(m,
         "RunPartOpt",
         "Options controlling the execution of run_part()."
     )