remove non required install for building documentation (#22)

* remove non-required install for building documentation
* get package automatically in setup.py
* rewrite requirement files

.github/workflows/docs.yml

@@ -25,8 +25,6 @@ jobs:
       - name: Build
         run: |
           sudo apt-get install graphviz
-          pip install git+https://github.com/embodied-computation-group/systole.git@dev
-          pip install .
           pip install -r requirements-docs.txt
           sphinx-build -b html docs/source docs/build/html
 

.github/workflows/test.yml

@@ -23,9 +23,7 @@ jobs:
           ${{ runner.os }}-pip-
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt
         pip install -r requirements-tests.txt
-        pip install .
         pip install ipykernel coverage pytest pytest-cov
         python -m ipykernel install --user --name python3
     - name: Run tests and coverage

requirements-docs.txt

@@ -1,11 +1,9 @@
+-e .
 xarray>=2022.6.0
-pymc>=5.0.1
-matplotlib>=3.0.2
 jupyter_sphinx>=0.4.0
 pydata-sphinx-theme>=0.12.0
 sphinx-bootstrap-theme>=0.8.1
 sphinxcontrib-bibtex>=2.4.2
-sphinx-gallery>=0.11.0
 myst-nb>=0.16.0
 sphinx>=5.3.0
 numpydoc>=1.4.0

requirements-tests.txt

@@ -1 +1,2 @@
+-e .
 seaborn>=0.11.2

requirements.txt

@@ -1,7 +1,10 @@
-numpy>=1.17
-numba>=0.51.2
-matplotlib>=3.4.3
+numpy>=1.18,<=1.23
+numba>=0.56.4
+matplotlib>=3.0.2
+seaborn>=0.9.0
 arviz>=0.12.0
 pymc>=5.0.0
 jax<=0.4.1
-jaxlib<=0.4.1
+jaxlib<=0.4.1
+setuptools>=38.4
+packaging

setup.py

@@ -1,8 +1,14 @@
 import codecs
 import os
 
-from setuptools import setup
+from setuptools import setup, find_packages
 
+PROJECT_ROOT = os.path.dirname(os.path.realpath(__file__))
+REQUIREMENTS_FILE = os.path.join(PROJECT_ROOT, "requirements.txt")
+
+def get_requirements():
+    with codecs.open(REQUIREMENTS_FILE) as buff:
+        return buff.read().splitlines()
 
 # Get the package's version number of the __init__.py file
 def read(rel_path):
@@ -31,13 +37,7 @@ def get_version(rel_path):
 DISTNAME = "ghgf"
 AUTHOR = "ILAB"
 MAINTAINER = "Nicolas Legrand"
-MAINTAINER_EMAIL = "nicolas.legrand@cfin.au.dk"
-INSTALL_REQUIRES = [
-    "jax>=0.3.13",
-    "jaxlib>=0.3.10",
-]
-PACKAGES = ["ghgf"]
-
+MAINTAINER_EMAIL = "nicolas.legrand@cas.au.dk"
 
 
 if __name__ == "__main__":
@@ -53,8 +53,8 @@ def get_version(rel_path):
         long_description_content_type="text/x-rst",
         license="GPL-3.0",
         version=get_version("ghgf/__init__.py"),
-        install_requires=INSTALL_REQUIRES,
+        install_requires=get_requirements(),
         include_package_data=True,
         package_data={"": ["ghgf/ghgf/data/*.dat"]},
-        packages=PACKAGES,
+        packages=find_packages(),
     )