First update to many of the base configuration files to better match …

.gitignore

@@ -44,6 +44,8 @@ docs/_build
 #  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/
+.eclipse
+.vscode
 .spyderproject
 .spyproject
 
@@ -67,3 +69,6 @@ venv.bak/
 *.swp
 *.swo
 *.orig
+
+# testing
+test_models/

CITATION.cff

@@ -3,14 +3,17 @@
 cff-version: "1.2.0"
 title: "dgl_abm"
 authors:
-  - family-names: Grootes
-    given-names: Meiert
+  - family-names: Atlas
+    given-names: Team
     orcid: "https://orcid.org/0000-0000-0000-0000"
-date-released: 2024-10-25
+date-released: 20??-MM-DD
+doi: <insert DOI here>
 version: "0.1.0"
 repository-code: "https://github.com/SDCCA/dgl_abm"
 keywords:
   - "ABM"
-  - " Tensor"
-  - " PyTorch"
+  - "Graph"
+  - "PyTorch"
+  - "Tensor"
 message: "If you use this software, please cite it using these metadata."
+license: Apache-2.0

NOTICE

@@ -1,2 +1,2 @@
 This product includes dgl_abm, software developed by
-Meiert W. Grootes.
+Netherlands eScience Center.

README.dev.md

@@ -60,7 +60,9 @@ To see the results on the command line, run
 coverage report
 ```
 
-`coverage` can also generate output in HTML and other formats; see `coverage help` for more information.## Running linters locally
+`coverage` can also generate output in HTML and other formats; see `coverage help` for more information.
+
+## Running linters locally
 
 For linting and sorting imports we will use [ruff](https://beta.ruff.rs/docs/). Running the linters requires an
 activated virtual environment with the development tools installed.
@@ -71,9 +73,14 @@ ruff check .
 
 # linter with automatic fixing
 ruff check . --fix
+
+# linter with reformatting enabled
+ruff format .
 ```
 
-To fix readability of your code style you can use [yapf](https://github.com/google/yapf).## Generating the API docs
+To fix readability of your code style you can use [yapf](https://github.com/google/yapf).
+
+## Generating the API docs
 
 ```shell
 cd docs
@@ -113,6 +120,15 @@ bump-my-version bump minor  # bumps from e.g. 0.3.2 to 0.4.0
 bump-my-version bump patch  # bumps from e.g. 0.3.2 to 0.3.3
 ```
 
+The code also compares stored model versions to the current code version when loading existing models.
+
+Updating the current code version, stored in `src/version.md` is done with a script:
+
+```shell
+cd src
+regen_version.sh
+```
+
 ## Making a release
 
 This section describes how to make a release in 3 parts:

README.md

@@ -22,13 +22,14 @@ The project setup is documented in [project_setup.md](project_setup.md). Feel fr
 
 ## Installation
 
-To install dgl_abm from GitHub repository, do:
+To install dgl_abm from GitHub repository*, do:
 
 ```console
 git clone [email protected]:SDCCA/dgl_abm.git
 cd dgl_abm
 python -m pip install .
 ```
+\* - the project is currently under development and is not release-ready yet.
 
 ## Documentation
 

environment_cuda.yaml

@@ -0,0 +1,11 @@
+# To run dgl_ptm on an infra with NVIDIA GPUs, you need to install cuda version
+# of dgl. This environment file specifies the dgl conda channel and cuda version
+# of dgl.
+name: dgl_abm_cuda
+channels:
+  - defaults
+dependencies:
+  - python>=3.11,<3.12
+  - dglteam/label/cu121::dgl
+  - pip:
+    - -e ./dgl_abm  # install dgl_abm in the editable mode, # TODO change to the actual pypi packages

project_setup.md

@@ -11,7 +11,6 @@ checklist](https://guide.esciencecenter.nl/#/best_practices/checklist).
 
 This repository is set up with Python versions:
 
-- 3.10
 - 3.11
 - 3.12
 
@@ -57,7 +56,8 @@ help you decide which tool to use for packaging.
 - The documentation is set up with the ReadTheDocs Sphinx theme.
   - Check out its [configuration options](https://sphinx-rtd-theme.readthedocs.io/en/latest/).
 - [AutoAPI](https://sphinx-autoapi.readthedocs.io/) is used to generate documentation for the package Python objects.
-- `.readthedocs.yaml` is the ReadTheDocs configuration file. When ReadTheDocs is building the documentation this package and its development dependencies are installed so the API reference can be rendered.- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=writingdocumentation)
+- `.readthedocs.yaml` is the ReadTheDocs configuration file. When ReadTheDocs is building the documentation this package and its development dependencies are installed so the API reference can be rendered.
+- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=writingdocumentation)
 
 ## Coding style conventions and code quality
 

pyproject.toml

@@ -9,7 +9,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 authors = [
-    { name = "Meiert W. Grootes", email = "[email protected]" }
+    {name = "Meiert W. Grootes", email = "[email protected]"},
+    {name = "Debraj Roy"},
+    {name = "Fakhereh Sarah Alidoost"},
+    {name = "Pranav Chandramouli"},
+    {name = "Thijs van Lankveld"},
 ]
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
@@ -18,17 +22,28 @@ classifiers = [
     "",
     "Natural Language :: English",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
-dependencies = []
+dependencies = [
+    "dask",
+    "dgl",
+    "numpy",
+    "pydantic>=2",
+    "scipy==1.10.1",
+    "torch==2.1.1",
+    "torchdata==0.7.1",
+    "torchvision",
+    "torchaudio",
+    "xarray",
+    "zarr",
+]
 description = "ABM modelling framework using networks and tensor algebra supported by the DGL library"
-keywords = ["ABM"," Tensor"," PyTorch"]
+keywords = ["ABM", "Graph", "PyTorch", "Tensor"]
 license = {file = "LICENSE"}
 name = "dgl_abm"
 readme = {file = "README.md", content-type = "text/markdown"}
-requires-python = ">=3.8"
+requires-python = ">=3.11, <3.12"
 version = "0.1.0"
 
 [project.optional-dependencies]
@@ -85,7 +100,7 @@ extras = dev
 [tool.ruff]
 line-length = 120
 output-format = "concise"
-extend-exclude = ["docs"]
+extend-exclude = ["docs", "build"]
 
 [tool.ruff.lint]
 # Allow unused variables when underscore-prefixed.

src/regen_version.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+git rev-parse HEAD > version.md
+

src/version.md

@@ -0,0 +1 @@
+9b09149e38a6ae5c9889e0418d4520fa74b5c551