Merge pull request #54 from DeepLearnPhysics/docs

Docs update

.github/workflows/release.yaml

@@ -0,0 +1,37 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v2
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine pytest
+        sudo apt-get install libhdf5-serial-dev
+        pip install -r requirements.txt
+        git submodule update --init
+    # - name: Build manylinux Python wheels
+    #   uses: RalfG/python-wheels-manylinux-build@v0.5.0-manylinux2014_x86_64
+    #   with:
+    #     python-versions: 'cp36-cp36m'
+    #     build-requirements: 'scikit-build numpy h5py cmake'
+    #     system-packages: 'hdf5-devel'
+    #     # pre-build-command: 'sh pre-build-script.sh'
+    #     # package-path: 'my_project'
+    #     # pip-wheel-args: '-w ./dist --no-deps'
+    - name: Build and publish Source Dist
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist
+        twine upload dist/*
+

.github/workflows/test.yaml

@@ -0,0 +1,32 @@
+name: Test Larcv
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine pytest
+          sudo apt-get install libhdf5-serial-dev
+          pip install -r requirements.txt
+          git submodule update --init
+      - name: Build and Install
+        run: |
+          python setup.py build -j 1
+          python setup.py install --user
+      - name: Test with pytest
+        run: |
+          pytest -m "not distributed_test" tests/

larcv/__init__.py

@@ -4,6 +4,8 @@
 import os
 from . _version import __version__
 
+from . config_builder import ConfigBuilder
+
 def get_includes():
     return os.path.dirname(__file__) + "/include/"
 

larcv/_version.py

@@ -1 +1 @@
-__version__ = "3.4.2"
+__version__ = "3.4.2.2"

larcv/config_builder.py

@@ -3,6 +3,10 @@
 import uuid
 
 class ConfigBuilder:
+    """
+    Front-end to create configuration objects step by step.
+    """
+
 
     valid_datatypes = \
         [ f"tensor{i+1}d" for i in range(4) ] + \
@@ -21,11 +25,18 @@ class ConfigBuilder:
     def __init__(self):
         self.config = larcv.QueueProcessor.default_config()
 
-    def get_config(self): return self.config
+    def get_config(self):
+        """
+        Gets the configuration.
+        
+        :returns:   The configuration.
+        
+        """
+        return self.config
 
     def set_parameter(self,value,*keys):
         """
-        Sets the parameter to value, walking into the config dictionare in the order of keys
+        Sets the parameter to value, walking into the config dictionary in the order of keys
 
         :param      value:  The value
         :type       value:  { type_description }
@@ -40,6 +51,10 @@ def set_parameter(self,value,*keys):
         return
 
     def print_config(self):
+        """
+        Prints a configuration using json to format it.
+        
+        """
         return json.dumps(self.config, indent=2)
 
     def validate_datatype(self, datatype : str):
@@ -69,15 +84,15 @@ def add_preprocess(self, datatype : str, producer : str, process : str, name : s
         """
         Adds a preprocess.
 
-        :param      datatype:  The datatype
+        :param      datatype:  The datatype of the input
         :type       datatype:  str
-        :param      producer:  The producer
+        :param      producer:  The producer of the input
         :type       producer:  str
-        :param      process:   The process
+        :param      process:   The process name
         :type       process:   str
-        :param      name:      The name
+        :param      name:      The name of the process in the config (optional)
         :type       name:      str
-        :param      kwargs:    The keywords arguments
+        :param      kwargs:    The keywords arguments to override and parameters in the preprocess
         :type       kwargs:    dictionary
         """
 
@@ -148,13 +163,13 @@ def add_batch_filler(self, datatype : str, producer : str, name : str = "", **kw
         """
         Adds a preprocess.
 
-        :param      datatype:  The datatype
+        :param      datatype:  The datatype to load into memory
         :type       datatype:  str
-        :param      producer:  The producer
+        :param      producer:  The producer of the datatype
         :type       producer:  str
-        :param      name:      The name
+        :param      name:      The name of the process in the config file (optional)
         :type       name:      str
-        :param      kwargs:    The keywords arguments
+        :param      kwargs:    Any override arguments to the configuration
         :type       kwargs:    dictionary
         """
 

pyproject.toml

@@ -0,0 +1,3 @@
+
+[build-system]
+requires = ["numpy", "scikit-build", "h5py", "cmake"]

setup.py

@@ -40,20 +40,15 @@
 else:
     pybind_value='ON'
 
-if 'MAKE_DOCS' in os.environ and os.environ['MAKE_DOCS']:
-    docs_value='ON'
-else:
-    docs_value='OFF'
 
 # Speed up the build if not directly set:    
 if 'MAKEFLAGS' not in os.environ: 
-    os.environ['MAKEFLAGS'] = "-j"
+    os.environ['MAKEFLAGS'] = "-j 1" # This lets builds on CI work better.
 
 setup(
     name="larcv",
     version=verstr,
     cmake_source_dir='src/',
-    use_scm_version=True,
     include_package_data=True,
     cmake_args=[
         '-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9',
@@ -62,7 +57,6 @@
         # '-DMPI_C_COMPILER={}'.format(mpicc),
         '-DMPI:BOOL={}'.format(mpi_value),
         '-DOPENMP:BOOL={}'.format(openmp_value),
-        '-DDOCS:BOOL={}'.format(docs_value),
         f'-DCMAKE_PYVERSION={py_version}'
     ],
     author=['Corey Adams', 'Kazuhiro Terao', 'Taritree Wongjirad', 'Marco del Tutto'],
@@ -77,8 +71,10 @@
     scripts=['bin/merge_larcv3_files.py', 'bin/run_processor.py'],
     packages=['larcv','src/pybind11'],
     install_requires=[
-        'numpy',
-        'scikit-build',
+        "numpy",
+        "scikit-build",
+        "h5py",
+        "cmake",
     ],
     long_description=long_description,
     long_description_content_type='text/markdown',

src/CMakeLists.txt

@@ -63,7 +63,7 @@ include_directories(json/include)
 if(CMAKE_PYTHON_BINDINGS)
 
   # Many packages need python:
-  find_package(Python ${CMAKE_PYVERSION} EXACT REQUIRED COMPONENTS  Interpreter Development)
+  find_package(Python ${CMAKE_PYVERSION} REQUIRED COMPONENTS  Interpreter Development)
   include_directories(${Python_INCLUDE_DIRS})
 
   message("Adding pybind11")