Merge pull request #3 from artificial-life-lab/env-test

Version locked dependencies requirements file

.github/workflows/test_and_deploy.yml

@@ -22,8 +22,8 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.7, 3.8]
+        platform: [ubuntu-latest]
+        python-version: [3.10.12]
 
     steps:
       - uses: actions/checkout@v2
@@ -42,17 +42,6 @@ jobs:
             libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
             libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
 
-      # strategy borrowed from vispy for installing opengl libs on windows
-      - name: Install Windows OpenGL
-        if: runner.os == 'Windows'
-        run: |
-          git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
-
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -79,7 +68,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.x"
+          python-version: "3.xx.xx"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

README.md

@@ -10,13 +10,15 @@ Library to conduct experiements on population dynamics.
 
 ## Installation
 
-- To generate required log and results directories, run
+- To generate required log and results directories and setup virtual environment, run
 
 ```(bash)
 bash init.sh
 ```
+This step needs to be performed only once to set up your work space.
+
+- Alternatively, you can create virtual environment manually as follows:
 
-- Create virtual environment
 ```bash
 mkdir -p ~/venvs/population-dynamics
 python3 -m venv ~/venvs/population-dynamics
@@ -36,8 +38,10 @@ pip install --upgrade pip setuptools
 ```bash
 pip install -r requirements.txt
 ```
+Alternatively, there exists `requirements_lock.txt` to get a version of the environment that is tested by us in terms of dependencies. The downside of using this file to installing dependencies is that you might not get all the latest version of packages.
+In case, if either or the files do not setup the environment successfully, please raise an issue.
 
-- Install `causal_inference` as a package within the environment
+- Install `causal_inference` as a package within the environment in development setting if you want to use the repo in the development mode by running the following line
 
 ```(bash)
 python setup.py develop
@@ -54,5 +58,6 @@ You can edit the `config.py` file directly to play around with the parameter val
 ```(bash)
 python causal_inference/base/lv_simulator.py
 ```
+This will take all the default arguments and configuration to run a simulation instance of lotka-volterra population dynamics.
 
-- The simulation statistics will be saved in the `repo/results` directory.
+- The simulation statistics will be saved in the `repo/results` directory by default.

causal_inference/tests/test_lv_simulator.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # flake8: noqa
-from causal_inference import LotkaVolterra
-from causal_inference import LV_PARAMS
+from causal_inference.base.lv_system import LotkaVolterra
+from causal_inference.config import LV_PARAMS
 
 def test_lotka_volterra():
     model = LotkaVolterra()

init.sh

@@ -1,4 +1,8 @@
 #!/bin/bash
 
-# Create folders for logging results
+# Create folders for virtual environment and logging results
 mkdir -p results
+mkdir -p .venv
+
+# Create Virtual env
+python3 -m venv .venv

requirements.txt

@@ -1,3 +1,4 @@
 numpy
 h5py
-matplotlib
+matplotlib
+scipy

requirements_lock.txt

@@ -0,0 +1,28 @@
+autocommand==2.2.2
+backports.tarfile==1.2.0
+-e git+ssh://git@github.com/artificial-life-lab/population-dynamics.git@a964a35de85d47c6e39550c87d552a4ffe73d200#egg=causal_inference_population_dynamics
+contourpy==1.3.1
+cycler==0.12.1
+fonttools==4.54.1
+h5py==3.12.1
+importlib_metadata==8.0.0
+inflect==7.3.1
+jaraco.collections==5.1.0
+jaraco.context==5.3.0
+jaraco.functools==4.0.1
+jaraco.text==3.12.1
+kiwisolver==1.4.7
+matplotlib==3.9.2
+more-itertools==10.3.0
+numpy==2.1.3
+packaging==24.2
+pillow==11.0.0
+platformdirs==4.2.2
+pyparsing==3.2.0
+python-dateutil==2.9.0.post0
+scipy==1.14.1
+six==1.16.0
+tomli==2.0.1
+typeguard==4.3.0
+typing_extensions==4.12.2
+zipp==3.19.2

tox.ini

@@ -1,28 +1,21 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{37,38,39}-{linux,macos,windows}
+envlist = py{310}-{linux}
 
 [gh-actions]
 python =
-    3.7: py37
-    3.8: py38
-    3.9: py39
+    3.10.12: py310
 
 [gh-actions:env]
 PLATFORM =
     ubuntu-latest: linux
-    macos-latest: macos
-    windows-latest: windows
 
 [testenv]
-platform = 
-    macos: darwin
+platform =
     linux: linux
-    windows: win32
 passenv = 
     CI
     GITHUB_ACTIONS
-    DISPLAY XAUTHORITY
     NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
     PYVISTA_OFF_SCREEN
 deps =