add url handling (#24)

* support custom dependencies

* add tests

* fmt

* add generate_environment function and allow additional list of requirements

* simplify and add tests

* simplify

* refactor

* update create_from_definition

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update generate_environment.py

* Update generate_environment.py

* use package name in pip requirements again

a relative local directory has du be indicated like file:/../directory

* update tests and local pip handling

* simplify

* add docstrings

* fix

* fix pip formatting

* ad definition test

* update readme

* add missing file

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/test.yml

@@ -1,6 +1,21 @@
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
+  pytest:
+    name: pytest
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    - name: pip install package
+      run: pip install .[test]
+    - name: run pytest
+      run: pytest
+
   demo_job:
     name: action
     runs-on: ${{ matrix.os }}

.gitignore

@@ -0,0 +1,167 @@
+# custom folders
+demo/
+
+pydeps2env/_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

README.md

@@ -1,7 +1,7 @@
 # pydeps2env
 
 An easy way to create conda environment files from you python project dependencies.  
-Creates a conda `environment.yml` file from python package dependencies listed in a `pyproject.toml` or `setup.cfg` file.
+Creates a conda `environment.yml` file from python package dependencies listed in on or multiple different source formats like `pyproject.toml`, `setup.cfg`, `environment.yaml` or `requirements.txt` files.
 
 The project contains
 - GitHub action
@@ -42,7 +42,7 @@ test = ["pytest"]
 pip_only = ["bidict"]
 ```
 
-The default parameters will output this sorted `environment.yml` (note that the `python` dependency will always be the first item on the list):
+The default parameters will output this sorted `environment.yml` (note that the `python` dependency specification will always be the first item on the list):
 
 ```yaml
 channels:
@@ -74,13 +74,71 @@ dependencies:
     - bidict
 ```
 
-## configuration options
+## basic usage (python)
+
+Create an `Environment` using Python and export it to an `environment.yaml` file.
+
+```python
+from pydeps2env import Environment
+
+env = Environment("./test/pyproject.toml[doc]")
+env.export("my_environment.yaml")
+```
+
+## basic usage (command line)
+
+Combine multiple source files into a single environment file (including build dependencies).
+Install pandas using `pip`.
+
+```bash
+pydeps2env ./test/setup.cfg ./test/pyproject.toml[doc] ./test/environment.yaml ./test/requirements.txt -o output.yaml -c defaults --extras test -b include --pip pandas
+```
+
+## advanced usage (definition file)
+
+Users can store complex configurations in a single yaml file and create the desired output using `create_from_definition`.
+Example definition file:
+
+```yaml
+# the target file to create
+output: test-configuration.yaml
+# default name of the environment
+name: test-env
+# conda channels to include
+channels:
+- conda-forge
+- defaults
+# list of source files that define sub environments
+# these will be loaded as Environment()
+sources:
+- ./test/environment.yaml
+- ./test/local.yaml
+- ./test/pyproject.toml[doc]
+- ./test/requirements.txt
+- https://github.com/CagtayFabry/pydeps2env/blob/custom_deps/pyproject.toml
+# extras to apply to all sources and packages
+extras:
+- test
+# dependencies that should be removed after collection
+remove:
+- pyyaml
+additional_requirements:
+- urllib3
+# include build system dependencies
+# list of dependencies that must be pip installed (excluding auto-sorted depedencies like urls)
+pip:
+- urllib3
+include_build_system: include
+
+```
+
+## configuration options (GitHub action)
 
 To customize the output the input options are available to the action:
 
 ### files
 
-Specify the location of the `'setup.cfg'` or `'pyproject.toml'` files to parse. (defaults to `'pyproject.toml'`)
+Specify the location of the dependencies files to parse. (defaults to 'pyproject.toml')
 Multiple files can be listed. This will result in a combined environment file.
 
 ### output:
@@ -105,7 +163,8 @@ is `'omit'` so no setup dependencies will be installed).
 
 ### pip
 List of packages to install via `pip` instead of `conda`.
-The dependencies will be listet under the `pip:` section in the environment file.
+The dependencies will be listed under the `pip:` section in the environment file.
+If a dependency is listed with its URN, it will always be installed via pip (e.g. `pydeps2env @ git+https://github.com/CagtayFabry/pydeps2env`)
 
 ## example
 

action.yml

@@ -7,6 +7,7 @@ inputs:
   files:
     description: >-
       Specify the location of the dependencies files to parse. (defaults to 'pyproject.toml')
+      Separate a list of multiple source files by spaces (e.g. 'pyproject.toml[test] requirements.txt').
     required: true
     default: pyproject.toml
   output:
@@ -16,25 +17,27 @@ inputs:
     default: environment.yml
   channels:
     description: >-
-      List the conda channels to include in the environment file. (defaults to 'defaults')
+      List the conda channels to include in the environment file. (defaults to 'conda-forge')
       Separate a list of multiple channels by spaces (e.g. 'conda-forge defaults').
     required: true
-    default: defaults
+    default: conda-forge
   extras:
     description: >-
-      Specify one or more optional [extras_require] sections to add to the environment
-      (e.g. 'test' to include package that you would normally install with 'pip install pkg[test]')
+      Specify one or more optional [extras_require] sections to add to all source files (s.a.).
+      (e.g. 'test' to include package that you would normally install with 'pip install pkg[test]').
+      Note that for individual sources in 'files', the '[extra]' syntax is also possible.
     required: false
   build_system:
     description: >-
-      if set to 'include' the dependencies listed under [build-system] or [options]:setup_requires will be added to the environment
-      (default is 'omit' so no setup dependencies will be installed)
+      if set to 'include' the dependencies listed under [build-system] (for 'pyproject.toml') or [options]:setup_requires (for 'setup.cfg') will be added to the environment
+      (default is 'omit' so no build system dependencies will be installed)
     required: false
     default: omit
   pip:
     description: >-
       List of packages to install via pip instead of conda.
       The dependencies will be listet under the pip section in the environment file.
+      If a dependency is listed with its URN, it will always be installed via pip (e.g. 'pydeps2env @ git+https://github.com/CagtayFabry/pydeps2env')
     required: false
 runs:
   using: composite

pydeps2env/__init__.py

@@ -1,8 +1,18 @@
 """pydeps2env: helps to generate conda environment files from python package dependencies."""
 
 from .environment import Environment
+from .generate_environment import (
+    create_environment,
+    create_environment_file,
+    create_from_definition,
+)
 
-__all__ = ["Environment"]
+__all__ = [
+    "Environment",
+    "create_environment",
+    "create_environment_file",
+    "create_from_definition",
+]
 
 try:
     from ._version import __version__