Merge pull request #232 from OSeMOSYS/master

Updating Development Branch

.github/workflows/python-publish.yml

@@ -0,0 +1,40 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox
+    - name: Build package
+      run: tox -e build
+    - name: Publish package
+      run: tox -e publish
+      env:
+        TWINE_USERNAME: ${{ vars.TWINE_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
+        TWINE_REPOSITORY: ${{ vars.TWINE_REPOSITORY }}

.github/workflows/python.yaml

@@ -5,10 +5,11 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest]
 
     steps:
       - uses: actions/checkout@v3
@@ -20,17 +21,14 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install tox
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          pip install -e .
       - name: Lint with flake8
         run: |
           tox -e lint
-      - name: Test with pytest
+      - name: Run tests using tox
         run: |
           tox
       - name: Upload coverage data to converalls.io
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          pip install --upgrade coveralls
-          coveralls --service=github
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+        uses: coverallsapp/github-action@v2

.pre-commit-config.yaml

@@ -53,7 +53,7 @@ repos:
   ## You can add flake8 plugins via `additional_dependencies`:
   #  additional_dependencies: [flake8-bugbear]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961  # Use the sha / tag you want to point at
+    rev: v1.9.0  # Use the sha / tag you want to point at
     hooks:
     -   id: mypy
         additional_dependencies: ['types-PyYAML']

.readthedocs.yml

@@ -8,16 +8,16 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF
 formats:
   - pdf
 
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - {path: ., method: pip}
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"

.zenodo.json

@@ -1,25 +1,17 @@
 {
+    "title": "otoole: OSeMOSYS Tools for Energy Work",
     "license": "MIT",
     "upload_type": "software",
     "creators": [
-        {
-            "name": "Will Usher",
-            "affiliation": "KTH Royal Institute of Technology",
-            "orcid": "0000-0001-9367-1791"
-        },
         {
             "name": "Trevor Barnes",
             "affiliation": "Simon Fraser University",
             "orcid": "0000-0003-2458-2968"
         },
         {
-            "name": "Hauke Henke",
+            "name": "Will Usher",
             "affiliation": "KTH Royal Institute of Technology",
-            "orcid": "0000-0003-0098-8701"
-        },
-        {
-            "name": "Christoph Muschner",
-            "orcid": "0000-0001-8144-5260"
+            "orcid": "0000-0001-9367-1791"
         }
     ],
     "access_right": "open"

CHANGELOG.rst

@@ -2,6 +2,38 @@
 Changelog
 =========
 
+(Development) Version 1.1.3
+===========================
+- Lock pandas to 2.1.4 or later
+- Capital Investment result calculation fixed
+
+Version 1.1.2
+=============
+- Update zenodo metadata for JOSS
+
+Version 1.1.1
+=============
+- Fixes CPLEX result processing docs
+- Added joss status badge to readme
+- Fix Tests on Windows
+- Update graphviz install instructions
+
+Version 1.1.0
+=============
+- Public Python API added to call otoole directly in Python files
+- ReadCplex directly reads in CPLEX solution files. Drops the need to transform and sort solution files
+- ReadGlpk class added to process GLPK solution files
+- Update to Pydantic v2.0
+- ReadResultsCbc renamed to ReadWideResults
+- Model validation instructions updated in documentation
+- The ``--input_datafile`` argument is deprecated, and the user now must supply the input data to process results
+- Locks pandas to <2.1
+
+Version 1.0.4
+=============
+- Fixed issue with pydantic v2.0.0
+- Dropped support for Python 3.8. Otoole now requires Python 3.9 or later
+
 Version 1.0.3
 =============
 - Improved error message for multiple names mismatches

CITATION.cff

@@ -1,19 +1,36 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
+cff-version: "1.2.0"
 authors:
-  - family-names: Usher
-    given-names: Will
-    orcid: https://orcid.org/0000-0001-9367-1791
+- family-names: Barnes
+  given-names: Trevor
+  orcid: "https://orcid.org/0000-0003-2458-2968"
+- family-names: Usher
+  given-names: Will
+  orcid: "https://orcid.org/0000-0001-9367-1791"
+contact:
+- family-names: Barnes
+  given-names: Trevor
+  orcid: "https://orcid.org/0000-0003-2458-2968"
+doi: 10.5281/zenodo.10360538
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
   - family-names: Barnes
     given-names: Trevor
-    orcid: https://orcid.org/0000-0003-2458-2968
-  - family-names: Henke
-    given-names: Hauke
-    orcid: https://orcid.org/0000-0003-0098-8701
-  - family-names: Muschner
-    given-names: Christoph
-    orcid: https://orcid.org/0000-0001-8144-5260
-title: "otoole: OSeMOSYS tools for energy work"
-version: 1.0.0
-doi: 10.5281/zenodo.7677990
-date-released: 2023-02-26
+    orcid: "https://orcid.org/0000-0003-2458-2968"
+  - family-names: Usher
+    given-names: Will
+    orcid: "https://orcid.org/0000-0001-9367-1791"
+  date-published: 2023-12-20
+  doi: 10.21105/joss.05511
+  issn: 2475-9066
+  issue: 92
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 5511
+  title: "otoole: OSeMOSYS Tools for Energy Work"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.05511"
+  volume: 8
+title: "otoole: OSeMOSYS Tools for Energy Work"

README.rst

@@ -2,24 +2,46 @@
 otoole: OSeMOSYS tools for energy work
 ==================================================
 
+.. image:: https://joss.theoj.org/papers/e93a191ae795b171beff782a68fdc467/status.svg
+    :target: https://joss.theoj.org/papers/e93a191ae795b171beff782a68fdc467
+    :alt: JOSS status
+
+.. image:: https://img.shields.io/pypi/v/otoole.svg
+    :target: https://pypi.org/project/otoole/
+    :alt: PyPI
+
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :target: https://github.com/psf/black
+    :alt: Code Style
+
+.. image:: https://img.shields.io/badge/python-3.9_|_3.10_|_3.11-blue.svg
+    :target: https://crate.io/packages/otoole/
+    :alt: Python Version
+
+.. image:: https://img.shields.io/badge/License-MIT-green.svg
+    :target: https://opensource.org/licenses/MIT
+    :alt: License
+
+|
+
 .. image:: https://coveralls.io/repos/github/OSeMOSYS/otoole/badge.svg?branch=master&kill_cache=1
     :target: https://coveralls.io/github/OSeMOSYS/otoole?branch=master
+    :alt: Code Coverage
+
+.. image:: https://github.com/OSeMOSYS/otoole/actions/workflows/python.yaml/badge.svg?branch=master
+    :target: https://github.com/OSeMOSYS/otoole/actions/workflows/python.yaml
+    :alt: GitHub CI
 
 .. image:: https://readthedocs.org/projects/otoole/badge/?version=latest
     :target: https://otoole.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
-    :target: https://github.com/psf/black
-
-A Python toolkit to support use of OSeMOSYS
-
 Description
 ===========
 
 OSeMOSYS tools for energy work, or otoole, is a Python package
-which provides a command-line interface for users of OSeMOSYS. The aim of the
-package is to provide commonly used pre- and post-processing steps for OSeMOSYS.
+to support the users of OSeMOSYS. The aim of the package is to provide commonly
+used pre- and post-processing steps for OSeMOSYS.
 
 **otoole** aims to support different ways of storing input data and results,
 including csv files and Excel workbooks, as well as different implementations
@@ -49,5 +71,7 @@ Contributing
 
 New ideas and bugs `should be submitted <https://github.com/OSeMOSYS/otoole/issues/new>`_
 to the repository issue tracker. Please do contribute by discussing and developing these
-ideas further. To contribute directly to the documentation of code development, please see
-the contribution guidelines document.
+ideas further.
+
+To contribute directly to the code and documentation development, please see
+the `contribution guidelines <https://otoole.readthedocs.io/en/latest/contributing.html>`_.