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Merged
AndrewSazonov merged 2 commits into from
Mar 9, 2026
Merged

Apply updated templates and fix Zenodo DOI #116

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f31d7e1
Apply new templates
AndrewSazonov Mar 6, 2026
78b206e
Fix Zenodo DOI
AndrewSazonov Mar 6, 2026
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6 changes: 3 additions & 3 deletions .copier-answers.yml
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@@ -1,16 +1,16 @@
# WARNING: Do not edit this file manually.
# Any changes will be overwritten by Copier.
_commit: v0.10.0
_commit: v0.10.1-2-gd05af4f
_src_path: gh:easyscience/templates
app_docs_url: https://easyscience.github.io/dynamics-app
app_doi: 10.5281/zenodo.18163581
app_doi: 10.5281/zenodo.18877180
app_package_name: easydynamics_app
app_python: '3.12'
app_repo_name: dynamics-app
home_page_url: https://easyscience.github.io/dynamics
home_repo_name: dynamics
lib_docs_url: https://easyscience.github.io/dynamics-lib
lib_doi: 10.5281/zenodo.18163581
lib_doi: 10.5281/zenodo.18877180
lib_package_name: easydynamics
lib_python_max: '3.12'
lib_python_min: '3.11'
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14 changes: 6 additions & 8 deletions docs/docs/assets/javascripts/extra.js
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@@ -1,6 +1,5 @@
(function() {

"use strict"
;(function () {
'use strict'

// Variables
const header = document.getElementsByTagName('header')[0]
Expand All @@ -10,20 +9,19 @@
// Hide-show header shadow
function toggleHeaderShadow() {
if (window.pageYOffset <= 0) {
header.classList.remove("md-header--shadow")
header.classList.remove('md-header--shadow')
} else {
header.classList.add("md-header--shadow")
header.classList.add('md-header--shadow')
}
}

// Onload
window.onload = function() {
window.onload = function () {
toggleHeaderShadow()
}

// Onscroll
window.onscroll = function() {
window.onscroll = function () {
toggleHeaderShadow()
}

})()
18 changes: 12 additions & 6 deletions docs/docs/assets/javascripts/mathjax.js
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Expand Up @@ -3,21 +3,27 @@ window.MathJax = {
//inlineMath: [['\\(', '\\)']],
//displayMath: [['\\[', '\\]']],
// Add support for $...$ and \(...\) delimiters
inlineMath: [['$', '$'], ['\\(', '\\)']],
inlineMath: [
['$', '$'],
['\\(', '\\)'],
],
// Add support for $$...$$ and \[...]\ delimiters
displayMath: [['$$', '$$'], ['\\[', '\\]']],
displayMath: [
['$$', '$$'],
['\\[', '\\]'],
],
processEscapes: true,
processEnvironments: true
processEnvironments: true,
},
options: {
//ignoreHtmlClass: ".*|",
//processHtmlClass: "arithmatex"
// Skip code blocks only
skipHtmlTags: ['script','noscript','style','textarea','pre','code'],
skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre', 'code'],
// Only ignore explicit opt-out
ignoreHtmlClass: 'no-mathjax|tex2jax_ignore',
}
};
},
}

document$.subscribe(() => {
MathJax.startup.output.clearCache()
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2 changes: 1 addition & 1 deletion docs/docs/introduction/index.md
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Expand Up @@ -45,7 +45,7 @@ Zenodo, each with a version-specific Digital Object Identifier (DOI).

Citation details in various styles (e.g., APA, MLA) and formats (e.g.,
BibTeX, JSON) are available on the
[Zenodo archive page](https://doi.org/10.5281/zenodo.18163581).
[Zenodo archive page](https://doi.org/10.5281/zenodo.18877180).

## Contributing

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6 changes: 3 additions & 3 deletions pixi.toml
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Expand Up @@ -182,9 +182,9 @@ docs-update-assets = 'python tools/update_docs_assets.py'
# 📦 Template Management Tasks
##############################

copier-copy = "copier copy gh:easyscience/templates . --data-file .copier-answers.yml --data template_type=lib"
copier-recopy = "copier recopy --data-file .copier-answers.yml --data template_type=lib"
copier-update = "copier update --data-file .copier-answers.yml --data template_type=lib"
copier-copy = "copier copy gh:easyscience/templates . --data-file ../dynamics/.copier-answers.yml --data template_type=lib"
copier-recopy = "copier recopy --data-file ../dynamics/.copier-answers.yml --data template_type=lib"
copier-update = "copier update --data-file ../dynamics/.copier-answers.yml --data template_type=lib"
Comment on lines +185 to +187

@rozyczko rozyczko Mar 6, 2026

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Does this mean we also need to pull https://github.com/easyscience/dynamics?
How are we assuring this?

After installing dynamics-lib and running pixi run copier-copy I get

(sdk) C:\Users\piotr\projects\easy\dynamics-lib>pixi run copier-copy
✨ Pixi task (copier-copy in default): copier copy gh:easyscience/templates . --data-file ../dynamics/.copier-answers.yml --data template_type=lib                                                                Error: Argument of data-file expected to be ExistingFile, not '../dynamics/.copier-answers.yml':
    ValueError('../dynamics/.copier-answers.yml is not a file')

@AndrewSazonov AndrewSazonov Mar 6, 2026

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Yeah, we need to pull both dynamics and dynamics-lib. I described this process in the README in easyscience/templates.

Unfortunately, Copier cannot read the answers file from the web - it only supports local files 🙁. I tried to find a simple cross-platform workaround, but could not find a good solution.

I even wrote a script that downloads the answers file to a temporary location and then runs Copier using that file. But this introduced extra complexity and, in the end, was less maintainable than just having a few lines in the guide explaining the process.

Of course, I’m open to better alternatives if you have any suggestions.


#####################
# 🪝 Pre-commit Hooks
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2 changes: 2 additions & 0 deletions tools/add_spdx.py
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# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
# SPDX-License-Identifier: BSD-3-Clause
"""Add SPDX headers to Python files.

- SPDX-FileCopyrightText with the license holder name and organization
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2 changes: 2 additions & 0 deletions tools/check_spdx.py
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# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
# SPDX-License-Identifier: BSD-3-Clause
"""Check SPDX headers in Python files."""

from __future__ import annotations
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2 changes: 2 additions & 0 deletions tools/remove_spdx.py
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@@ -1,3 +1,5 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
# SPDX-License-Identifier: BSD-3-Clause
"""Remove SPDX headers from Python files."""

from __future__ import annotations
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2 changes: 2 additions & 0 deletions tools/test_scripts.py
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@@ -1,3 +1,5 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
# SPDX-License-Identifier: BSD-3-Clause
"""Test runner for tutorial scripts in the 'tutorials' directory.

This test discovers and executes all Python scripts located under the
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4 changes: 3 additions & 1 deletion tools/update_github_labels.py
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@@ -1,3 +1,5 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
# SPDX-License-Identifier: BSD-3-Clause
"""Set/update GitHub labels for current or specified easyscience
repository.

Expand All @@ -17,7 +19,7 @@
import argparse
import json
import shlex
import subprocess
import subprocess # noqa: S404
import sys
from dataclasses import dataclass

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