From 7aaaff10e343010fa198ff64c4278bc97fda3fce Mon Sep 17 00:00:00 2001
From: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com>
Date: Mon, 10 Jun 2024 15:10:59 +0200
Subject: [PATCH 1/2] Add publishing workflow inspired from the GEMDAT package.

---
 .github/workflows/publish.yaml     | 72 ++++++++++++++++++++++++++++++
 pyproject.toml                     | 36 +++++++++++----
 tools/generate_requirements_txt.py | 19 ++++++++
 3 files changed, 118 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/publish.yaml
 create mode 100644 tools/generate_requirements_txt.py

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
new file mode 100644
index 0000000..d92eef1
--- /dev/null
+++ b/.github/workflows/publish.yaml
@@ -0,0 +1,72 @@
+name: Publish on PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+
+jobs:
+  fix_release_deps:
+    permissions: write-all
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip pip-tools setuptools
+
+    - name: Set configuration
+      run: |
+        git config --global user.name "${GITHUB_ACTOR}"
+        git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+
+    - name: Create requirements files
+      run: |
+        python tools/generate_requirements_txt.py
+        pip-compile -o requirements_full.txt pyproject.toml
+        git add requirements_full.txt requirements.txt
+        git commit -m "Updated requirements.txt files" || true
+
+    - name: Bump version to new tag
+      run: |
+        python -m pip install bump-my-version
+        bump-my-version bump --new-version $GITHUB_REF_NAME patch
+        git commit -am "Bump version to: $GITHUB_REF_NAME"
+
+    - name: Push back changes to main and tag
+      run: |
+        git tag --force $GITHUB_REF_NAME HEAD
+        git push --force --tags
+        git switch -C main
+        git push --set-upstream -f origin main
+
+  deploy:
+    needs: fix_release_deps
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ github.ref_name }}
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build setuptools>=61.2 wheel
+        python -m build --no-isolation
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/pyproject.toml b/pyproject.toml
index 9a68c12..1690327 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,23 +27,41 @@ classifiers = [
 keywords = ["exoplanet", "atmosphere"]
 requires-python = '>=3.10'
 dependencies = [
-  'matplotlib',
-  'natsort',
-  'netcdf4',
-  'numpy',
-  'pandas',
-  'scipy',
-  'seaborn',
-  'tomlkit',
-  'f90nml' 
+  "matplotlib",
+  "natsort",
+  "netcdf4",
+  "numpy",
+  "pandas",
+  "scipy",
+  "seaborn",
+  "tomlkit",
+  "f90nml"
 ]
 
 [project.urls]
 homepage = "https://github.com/FormingWorlds/JANUS"
 
+[project.optional-dependencies]
+develop = [
+  "bump-my-version",
+  "pytest"
+]
+publishing = [
+  "wheel",
+  "build"
+]
+
 [tool.setuptools]
 package-dir = {"janus" = "src/janus"}
 include-package-data = true
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+
+[tool.bumpversion]
+current_version = "24.04.04"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = "version = \"{current_version}\""
+replace = "version = \"{new_version}\""
diff --git a/tools/generate_requirements_txt.py b/tools/generate_requirements_txt.py
new file mode 100644
index 0000000..a148c33
--- /dev/null
+++ b/tools/generate_requirements_txt.py
@@ -0,0 +1,19 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import tomllib
+
+this_script = Path(__file__)
+root = this_script.parents[1]
+pyproject = root / 'pyproject.toml'
+
+with open(pyproject, 'rb') as f:
+    metadata = tomllib.load(f)
+    dependencies = metadata['project']['dependencies']
+
+with open('requirements.txt', 'w') as f:
+    this_script_rel = this_script.relative_to(root)
+    f.write(f'# generated by {this_script_rel}\n')
+    f.write('\n'.join(dependencies))
+    f.write('\n')

From 8a2280b68c57b37073720d8bcaa064b5d079193e Mon Sep 17 00:00:00 2001
From: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com>
Date: Mon, 10 Jun 2024 15:51:09 +0200
Subject: [PATCH 2/2] Update pyproject.toml

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 1690327..34f4d07 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,6 +47,7 @@ develop = [
   "pytest"
 ]
 publishing = [
+  "twine",
   "wheel",
   "build"
 ]