Merge pull request #47 from fabian-sp/f-modernize-build

Modernize package structure and build

Author: fabian-sp

.github/workflows/unit_test.yml

@@ -19,13 +19,12 @@ jobs:
         with:
           activate-environment: gglasso_env
           environment-file: environment.yml
-          python-version: 3.8
+          python-version: 3.9
 
       # Install package and run tests
       - name: run tests
         # This one is very important so we can reuse conda env from last step
         shell: bash -l {0}
         run: |
-          pip install -e .
-          conda list
-          pytest gglasso/tests -v
+          python -m pip install --editable .
+          pytest tests/ -v

.readthedocs.yaml

@@ -22,6 +22,6 @@ formats:
 python:
    install:
     - requirements: readthedocs-requirements.txt
-    - method: setuptools
+    - method: pip
       path: .
 

README.md

@@ -25,28 +25,23 @@ or
     conda install -c conda-forge gglasso
 
 
-### Install from source
+### Developer installation
 
-Alternatively, you can install the package from source using the following commands:
+If you want to create a conda environment with full development dependencies (for building docs, testing,...), run:
 
-    git clone https://github.com/fabian-sp/GGLasso.git
-    pip install -r requirements.txt
-    python setup.py
+	conda env create -f environment.yml
 
-Test your installation with 
+To install `gglasso` in developer mode run
 
-    pytest gglasso/ -v
+    python -m pip install --editable .
 
 
-### Advanced options
+Test your installation with 
 
-If you want to create a conda environment with full development dependencies (for building docs, testing etc), run:
+    pytest tests/ -v
 
-	conda env create -f environment.yml
 
-If you wish to install `gglasso` in developer mode, i.e. not having to reinstall `gglasso` everytime the source code changes (either by remote or local changes), run
 
-    python setup.py clean --all develop clean --all
 
 ## The `glasso_problem` class
 

docs/source/getting-started.rst

@@ -6,29 +6,30 @@ Getting started
 Installation
 ^^^^^^^^^^^^^^^^
 
-``GGLasso`` is available over Pypi or `Github`_. For installation with pip, simply run 
+The official repository can be found on `Github`_. ``GGLasso`` is available over ``pip`` and ``conda``. For installation from PyPi, simply run 
 
 .. code-block::
 
      pip install gglasso
 
-To install from source, clone the repository and make sure you have all requirements installed. Then move to the directory and run
+For ``conda``, use
 
 .. code-block::
 
-     python setup.py
+     conda install -c conda-forge gglasso
 
-This installs a package called ``gglasso`` in your Python environment. In case you want to edit the source code and use the ``gglasso`` package without re-installing, you can run instead
+Alternatively, you can clone from Github and install a developer version with the command
 
 .. code-block::
 
-     python setup.py clean --all develop clean --all
+     python -m pip install --editable .
 
-To make sure that everything works properly you can run unit tests in ``gglasso/tests``, for example
+
+To make sure that everything works properly you can run unit tests with
 
 .. code-block::
 
-     pytest gglasso/ -v
+     pytest tests/ -v
 
 To import from ``GGLasso`` in Python, type for example
 

environment.yml

@@ -1,23 +1,20 @@
 name: gglasso_env
 
 dependencies:
-  - python>=3.8
-  - numpy>=1.19.2
-  - numba>=0.53.1
+  - python>=3.9
+  - numpy>=1.19.2, <2.0.0
+  - numba>=0.53.1, <0.60.0
   - scipy>=0.11.0
   - scikit-learn>=0.24.1
   - pandas
   - matplotlib
   - seaborn
   - networkx
-  - decorator==4.4.2
-  - sphinx==3.5.4
+  - sphinx
   - pytest
   - pip
   - pip:
     - regain
     - scikit-fda
-    - sphinx-gallery==0.8.2
-    - sphinx_rtd_theme==0.5.2
-    - fdasrsf==2.3.11
-  
+    - sphinx-gallery
+    - sphinx_rtd_theme

gglasso/__init__.py

@@ -0,0 +1,82 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+###############################################################################
+#                                 Main library                                #
+###############################################################################
+
+[project]
+name = "gglasso"
+dynamic = ["version"]
+description = 'Algorithms for Single and Multiple Graphical Lasso problems.'
+readme = "README.md"
+requires-python = ">=3.9"
+license = "MIT"
+keywords = ["network inference",
+            "graphcial models",
+            "graphical lasso",
+            "optimization"]
+authors = [
+  {name = "Fabian Schaipp", email = "[email protected]" },
+  {name = "Oleg Vlasovets", email = ""},
+  {name = "Christian L. Müller", email = ""},
+]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+]
+dependencies = [
+  "numpy>=1.17.3, <2.0.0",
+  "scipy>=0.11.0",
+  "scikit-learn>=0.24.1",
+  "numba>=0.46.0, <0.60.0",
+  "pandas",
+  "matplotlib",
+  "seaborn",
+  "networkx",
+]
+
+[project.urls]
+Documentation = "https://gglasso.readthedocs.io/en/stable/"
+Issues = "https://github.com/fabian-sp/GGLasso/issues"
+Source = "https://github.com/fabian-sp/GGLasso"
+
+[tool.hatch.version]
+path = "src/gglasso/__init__.py"
+
+[[tool.hatch.envs.all.matrix]]
+python = ["3.9", "3.10", "3.11", "3.12"]
+
+# The minimum Python version that should be supported
+target-version = "py39"
+
+[tool.hatch.build.targets.sdist]
+include = ["src/gglasso"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/gglasso"]
+
+###############################################################################
+#                           Development dependencies                          #
+###############################################################################
+
+# See: https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml
+[project.optional-dependencies]
+tests = ["pytest", "pytest-cov"]
+docs = [
+  "sphinx",
+  "sphinx-gallery",
+  "sphinx_rtd_theme",
+]
+examples = [
+  "regain",
+  "scikit-fda",
+]

pyproject.toml

@@ -4,4 +4,5 @@ sphinx
 sphinx-gallery
 sphinx_rtd_theme
 
-scikit-fda
+scikit-fda
+regain

readthedocs-requirements.txt

@@ -1,9 +1,8 @@
-numpy>=1.17.3
-numba>=0.46.0
+numpy>=1.17.3,<2.0.0
+numba>=0.46.0,<0.60.0
 scipy>=0.11.0
 scikit-learn>=0.24.1
 pandas
 matplotlib
 seaborn
 networkx
-regain

requirements.txt

@@ -10,14 +10,14 @@
 URL = 'https://github.com/fabian-sp/GGLasso'
 EMAIL = '[email protected]'
 AUTHOR = 'Fabian Schaipp'
-REQUIRES_PYTHON = '>=3.7.0'
+REQUIRES_PYTHON = '>=3.9.0'
 VERSION = gglasso.__version__
 
 
 # What packages are required for this module to be executed?
 REQUIRED = [
     "numpy>=1.17.3", "scipy>=0.11.0", "scikit-learn>=0.24.1", "numba>=0.46.0", "pandas",
-    "matplotlib", "seaborn", "networkx", "regain"]
+    "matplotlib", "seaborn", "networkx"]
 
 # What packages are optional?
 EXTRAS = {
@@ -27,6 +27,10 @@
             "sphinx-gallery",
             "sphinx_rtd_theme",
         ],
+        "examples": [
+            "regain",
+            "scikit-fda",
+        ]
     }
 
 here = os.path.abspath(os.path.dirname(__file__))
@@ -42,13 +46,12 @@
 
 CLASSIFIERS = """\
 Development Status :: 5 - Production/Stable
-Intended Audience :: Science/Research
-Intended Audience :: Developers
-License :: OSI Approved
+License :: OSI Approved :: MIT License
 Programming Language :: Python
-Programming Language :: Python :: 3
-Topic :: Software Development
-Operating System :: Unix
+Programming Language :: Python :: 3.9
+Programming Language :: Python :: 3.10
+Programming Language :: Python :: 3.11
+Programming Language :: Python :: 3.12
 """
 
 

setup.py

@@ -0,0 +1,2 @@
+__version__ = "0.2.1"
+