Sync with upstream LyoHUB/LyoPRONTO

.github/workflows/docs.yml

@@ -17,33 +17,31 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GIT_COMMITTER_NAME: ${{ github.actor }}
       GIT_COMMITTER_EMAIL: ${{ github.actor }}@users.noreply.github.com
+
     name: Deploy docs
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - name: Checkout main
+        uses: actions/checkout@v5
+        # To be able to push gh-pages branch later, need to have that branch fetched
+        # Could fetch it later on but this seems simpler and less finicky
         with:
           fetch-depth: 0
-      - name: Read CI version config
-        id: versions
-        uses: mikefarah/yq@v4.44.1
-        with:
-          cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ steps.versions.outputs.result }}
-      - run: pip install mkdocstrings-python mkdocs-material mike mkdocs-ipynb
+      - run: pip install .
+      - run: pip install .[docs]
       - run: echo ${{ github.event_name}} ${{ github.ref_name }}
       # Deploy docs according to type of event
-      - name: Deploy docs as latest
+      - name: Build docs as latest
         if: ${{ github.event_name == 'release' }}
         run: mike deploy ${{ github.ref_name }} latest
-      - name: Deploy docs for PR
+      - name: Build docs for PR
         if: ${{ github.event_name == 'pull_request' }}
         run: mike deploy pr-${{ github.event.number }}
-      - name: Deploy docs as dev
+      - name: Build docs as dev
         if: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
         run: mike deploy dev
-      - name: Get docs into GitHub Pages
+      - name: Deploy docs to GitHub Pages
+        if: ${{ github.event_name != 'pull_request' }}
         run: |
           git switch gh-pages
+          git push origin gh-pages

.github/workflows/pr-tests.yml

@@ -7,7 +7,7 @@ name: PR Tests
 
 on:
   pull_request:
-    branches: [ main, dev-pyomo ]
+    branches: [ main ]
     types: [ opened, synchronize, reopened, ready_for_review, converted_to_draft ]
 
 jobs:
@@ -26,11 +26,9 @@ jobs:
     - name: Determine test mode
       id: mode
       run: |
-        if [ "${{ github.event.pull_request.draft }}" == "true" ]; then
-          echo "coverage=false" >> $GITHUB_OUTPUT
+        if [ "${{ github.event.pull_request.draft }}" = "true" ]; then
           echo "mode=fast" >> $GITHUB_OUTPUT
         else
-          echo "coverage=true" >> $GITHUB_OUTPUT
           echo "mode=full" >> $GITHUB_OUTPUT
         fi
 
@@ -40,44 +38,31 @@ jobs:
         python-version: ${{ steps.versions.outputs.result }}
         cache: 'pip'
         cache-dependency-path: |
-          requirements.txt
-          requirements-dev.txt
+          pyproject.toml
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        pip install -r requirements.txt -r requirements-dev.txt
+        pip install .
+        pip install .[dev]
         pip install -e . --no-build-isolation
 
-    - name: Run tests (draft = fast, ready = coverage)
+    - name: Run tests
       run: |
-        if [ "${{ steps.mode.outputs.coverage }}" == "true" ]; then
-          echo "🔍 Running full tests with coverage (PR is ready for review)"
-          echo "⚡ Skipping slow tests (marked with @pytest.mark.slow) - these run on merge"
-          pytest tests/ -n auto -v -m "not slow" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+        if [ "${{ steps.mode.outputs.mode }}" == "fast" ]; then
+          echo "⚡ Draft PR - fast tests only (no notebook tests)"
+          pytest tests/ -n auto -v -m "not notebook"
         else
-          echo "⚡ Running fast tests without coverage (PR is draft)"
-          echo "⚡ Skipping slow tests (marked with @pytest.mark.slow)"
-          pytest tests/ -n auto -v -m "not slow"
+          echo "🔍 Full PR - running tests with coverage report"
+          pytest tests/ -n auto -v -m "not notebook" --cov-report=xml:coverage.xml
         fi
 
-    - name: Upload coverage (if run)
-      if: steps.mode.outputs.coverage == 'true'
+    - name: Upload coverage
+      if: steps.mode.outputs.mode == 'full'
       uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: pr-tests
         name: pr-coverage
         fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}
-
-    - name: Test Summary
-      if: always()
-      run: |
-        if [ "${{ steps.mode.outputs.coverage }}" == "true" ]; then
-          echo "✅ Full tests with coverage completed"
-          echo "📊 PR is ready for review with coverage verified"
-        else
-          echo "⚡ Fast tests completed (PR is draft)"
-          echo "� Mark PR as 'Ready for Review' to run coverage tests"
-        fi

.github/workflows/rundocs.yml

@@ -10,24 +10,54 @@ on:
 
 jobs:
   doctests:
-    # env:
-    #   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    #   GIT_COMMITTER_NAME: ${{ github.actor }}
-    #   GIT_COMMITTER_EMAIL: ${{ github.actor }}@users.noreply.github.com
-    name: Notebook
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: ./docs/examples
-    strategy:
-      matrix:
-        notebook: 
-         - knownRp_PD.ipynb
-         - unknownRp_PD.ipynb
+
     steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python
-        uses: actions/setup-python@v4
-      - run: pip install ruamel.yaml scipy numpy matplotlib papermill ipykernel
-      - name: Run notebooks
-        run: papermill ${{ matrix.notebook }} ${{ matrix.notebook }} -k python
+    - uses: actions/checkout@v4
+
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install -e . --no-build-isolation
+
+    - name: Run tests (draft = fast, ready = coverage)
+      run: pytest tests/ -n auto -v -m "notebook" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+# jobs:
+#   doctests:
+#     # env:
+#     #   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#     #   GIT_COMMITTER_NAME: ${{ github.actor }}
+#     #   GIT_COMMITTER_EMAIL: ${{ github.actor }}@users.noreply.github.com
+#     name: Notebook
+#     runs-on: ubuntu-latest
+#     defaults:
+#       run:
+#         working-directory: ./docs/examples
+#     strategy:
+#       matrix:
+#         notebook: 
+#          - knownRp_PD.ipynb
+#          - unknownRp_PD.ipynb
+#     steps:
+#       - uses: actions/checkout@v5
+#       - name: Set up Python
+#         uses: actions/setup-python@v4
+#       - run: pip install ruamel.yaml scipy numpy matplotlib papermill ipykernel
+#       - name: Run notebooks
+#         run: papermill ${{ matrix.notebook }} ${{ matrix.notebook }} -k python

.github/workflows/slow-tests.yml

@@ -36,13 +36,13 @@ jobs:
         python-version: ${{ steps.versions.outputs.result }}
         cache: 'pip'
         cache-dependency-path: |
-          requirements.txt
-          requirements-dev.txt
+          pyproject.toml
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        pip install -r requirements.txt -r requirements-dev.txt
+        pip install .
+        pip install .[dev]
         pip install -e . --no-build-isolation
 
     - name: Run slow tests

.github/workflows/tests.yml

@@ -24,13 +24,13 @@ jobs:
         python-version: ${{ steps.versions.outputs.result }}
         cache: 'pip'
         cache-dependency-path: |
-          requirements.txt
-          requirements-dev.txt
+          pyproject.toml
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        pip install -r requirements.txt -r requirements-dev.txt
+        pip install .
+        pip install .[dev]
         pip install -e . --no-build-isolation
 
     - name: Run ALL tests with pytest and coverage (including slow tests)

.gitignore

@@ -29,6 +29,11 @@ MANIFEST
 *.csv
 
 docs/build
+
+# for conda environment install, converted from pyproject.toml
+environment.yml 
+# for local settings
+.vscode/
 ################################################################################
 #                               Jupyter Notebook                               #
 ################################################################################

README.md

@@ -1,9 +1,3 @@
-# LyoPRONTO
-
-[![Tests](https://github.com/SECQUOIA/LyoPRONTO/workflows/Tests/badge.svg?branch=dev-pyomo)](https://github.com/SECQUOIA/LyoPRONTO/actions/workflows/tests.yml)
-[![Python 3.13](https://img.shields.io/badge/python-3.13-blue.svg)](https://www.python.org/downloads/)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![Code Coverage](https://img.shields.io/badge/coverage-93%25-brightgreen.svg)](htmlcov/index.html)
 
 LyoPRONTO is an open-source user-friendly tool to simulate and optimize freezing and primary drying in lyophilizers written using Python.
 
@@ -20,39 +14,9 @@ Execute:
 ```
 python3 LyoPronto.main -m
 ```
-LyoPRONTO is a vial-scale lyophilization (freeze-drying) process simulator written in Python. It models the freezing and primary drying phases using heat and mass transfer equations.
+This will execute the file `main.py` in an appropriate scope. Parameters can be changed in `main.py`. Files listing the inputs and outputs will be generated in the current directory, along with some plots of temperature, pressure, and drying progress vs. time.
 A video tutorial by the authors illustrating this process can be found [on LyoHUB's YouTube channel](https://youtu.be/DI-Gz0pBI0w).
 
-## Modern Examples
-
-For new users, we recommend using the examples in the `examples/` directory instead:
-```bash
-# Primary drying simulation (recommended starting point)
-python examples/example_web_interface.py
-
-# Parameter estimation from experimental data
-python examples/example_parameter_estimation.py
-
-# Process optimization
-python examples/example_optimizer.py
-
-# Freezing simulation
-python examples/example_freezing.py
-
-# Design space generation
-python examples/example_design_space.py
-```
-
-See [`examples/README.md`](examples/README.md) for detailed documentation.
-
-## Legacy Examples
-
-The repository root contains legacy example scripts for backward compatibility:
-- `ex_knownRp_PD.py` - Original primary drying example → Use `examples/example_web_interface.py` instead
-- `ex_unknownRp_PD.py` - Original parameter estimation example → Use `examples/example_parameter_estimation.py` instead
-
-These legacy scripts are maintained and tested, but new users should use the modern examples in the `examples/` directory.
-
 # Citation
 G. Shivkumar, P. S. Kazarin, A. D. Strongrich, & A. A. Alexeenko, "LyoPRONTO: An Open-Source Lyophilization PRocess OptimizatioN TOol",  AAPS PharmSciTech (2019) 20: 328. 
 
@@ -69,33 +33,3 @@ This program is distributed in the hope that it will be useful, but WITHOUT ANY
 You should have received a copy of the GNU General Public License along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 By request, this software may also be distributed under the terms of the GNU Lesser General Public License (LGPL); for permission, contact the authors or maintainer.
-
-# Documentation
-
-### Quick Start
-- **Getting Started**: [`docs/GETTING_STARTED.md`](docs/GETTING_STARTED.md) - Developer setup and environment
-- **Examples**: [`examples/README.md`](examples/README.md) - Web interface examples (primary drying, optimizer, freezing, design space)
-- **Testing**: [`tests/README.md`](tests/README.md) - Test suite (85 tests, 100% passing)
-
-### Technical Documentation
-- **Architecture**: [`docs/ARCHITECTURE.md`](docs/ARCHITECTURE.md) - System design and module structure
-- **Physics**: [`docs/PHYSICS_REFERENCE.md`](docs/PHYSICS_REFERENCE.md) - Equations, models, and thermodynamics
-- **Pyomo Integration**: [`docs/PYOMO_ROADMAP.md`](docs/PYOMO_ROADMAP.md) - NLP optimization plans
-- **Coexistence Philosophy**: [`docs/COEXISTENCE_PHILOSOPHY.md`](docs/COEXISTENCE_PHILOSOPHY.md) - Scipy + Pyomo parallel implementation
-
-### Development
-- **Development Log**: [`docs/DEVELOPMENT_LOG.md`](docs/DEVELOPMENT_LOG.md) - Chronological change history
-- **Contributing**: [`CONTRIBUTING.md`](CONTRIBUTING.md) - Contribution guidelines
-- **Archive**: [`docs/archive/`](docs/archive/) - Historical session summaries
-
-# Notes on contributing & maintenance
-
-There is a GitHub Action on this repo which will automatically build the documentation (which uses Material for MkDocs with `mike` for versioning). This action triggers on push to main (which creates a `dev` section of the docs), on publishing a release (which creates a numbered version of the docs), and on pull request edits (which makes a `pr-###` version of the docs). 
-After merging a pull request, it is a good idea to use [mike](https://github.com/jimporter/mike) to clear out the PR version of the docs. Locally, do something like the following
-```
-git fetch 
-mike delete pr-### # replace with correct PR number
-git switch gh-pages
-git push origin gh-pages
-```
-This could theoretically be automated but I decided against this for now. In the long run, it may be worth not generating PR versions of the docs if this is burdensome.

__init__.py

@@ -14,11 +14,4 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-
-import sys
-import scipy.optimize as sp
-import numpy as np
-import math
-import csv
-
 from .lyopronto import *