PyEnzyme v2.0.0

.github/workflows/lint.yml

@@ -0,0 +1,13 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "./pyenzyme"
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "./tests"

.github/workflows/unit-tests.yaml

@@ -0,0 +1,27 @@
+name: Unit Tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install pytest-cov openpyxl
+          pip3 install -e .
+      - name: Test with pytest
+        run: |
+          python3 -m pytest -v

.gitignore

@@ -131,15 +131,24 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# pyrightconfig
+pyrightconfig.json
+
 # pytype static type analyzer
 .pytype/
 
 # Cython debug symbols
 cython_debug/
 pyenzyme/Examples/getJSONValid.py
 
-# test dirs 
+# test dirs
 tests/tmp
 
 # PyCharm IDE
-.idea/
+.idea/
+
+# Mac OS
+.DS_Store
+
+# Poetry
+poetry.lock

Dockerfile

@@ -1,18 +1,11 @@
-FROM python:3.9
-WORKDIR /app
-
-COPY . /app
+FROM python:3.11.9-slim-bullseye
 
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends git \
-    && apt-get install -y --no-install-recommends gcc \
-    && apt-get install -y --no-install-recommends cmake \
-    && apt-get purge -y --auto-remove
+RUN apt-get update
+RUN pip install poetry
 
+WORKDIR /app
+COPY . /app
 
-RUN pip3 install git+https://github.com/EnzymeML/PyEnzyme.git
-RUN pip3 install fastapi uvicorn jinja2
-
-COPY pyenzyme_server.py /app
+RUN poetry install --with tests
 
-CMD ["uvicorn", "pyenzyme_server:app", "--host", "0.0.0.0", "--port", "80"]
+ENTRYPOINT ["poetry", "run", "pytest", "-vv"]

README.md

@@ -5,7 +5,7 @@
 </a>
 <a href="https://www.codacy.com/gh/EnzymeML/PyEnzyme/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=EnzymeML/PyEnzyme&amp;utm_campaign=Badge_Grade"><img src="https://app.codacy.com/project/badge/Grade/4ceb8d010e7b456c926c8b18737ff102"/></a>
 </h1>
-<p align="center"> 
+<p align="center">
 PyEnzyme is the interface to the data model <b>EnzymeML</b> and offers a convenient way to document and model research data. Lightweight syntax for rapid development of data management solution in enzymology and biocatalysis.</p>
 
 ### 🧬 Features
@@ -17,22 +17,27 @@ PyEnzyme is the interface to the data model <b>EnzymeML</b> and offers a conveni
 - **Visualize** experimental results for inspection and publication.
 
 ## ⚡️ Quick start
-Get started with PyEnzyme by running the following command 
+
+Get started with PyEnzyme by running the following command
 
 ```
 # Using PyPI
 python -m pip install pyenzyme
 ```
 
 Or build by source
+
 ```
 git clone https://github.com/EnzymeML/PyEnzyme.git
 cd PyEnzyme
 python3 setup.py install
 ```
 
 ### ⚙️ Package Options
-PyEnzyme comes with many flavors, choose whether you want only the base installation, the modeling package or all of it using the following options.
+
+PyEnzyme comes with many flavors, choose whether you want only the base installation, the modeling package or all of it
+using the following options.
+
 ```
 # COPASI - modeling
 python -m pip install "pyenzyme[copasi]"
@@ -53,71 +58,40 @@ python -m pip install "pyenzyme[dataverse]"
 python -m pip install "pyenzyme[all]"
 ```
 
-### 🚀 PyEnzyme's REST-API
-
-If you want to deploy PyEnzyme as a server and use our REST-API to access PyEnzyme from any HTTP-capable programming language, use our official [docker image](https://hub.docker.com/r/enzymeml/pyenzyme/tags) or simply copy and past the following.
-
-```bash
-docker pull enzymeml/pyenzyme:latest
-docker run -p 8000:8000 enzymeml/pyenzyme:latest
-```
-See the [API documentation](https://api.enzymeml.org) for details on our endpoints. You can also use our self-hosted PyEnzyme instance if you have no server space - Use https://api.enzymeml.org as base URL to the endpoints.
-
 ## ⚙️ Example code
 
-This example will demonstrate how to create a simple EnzymeML document using PyEnzyme and how to use initializers from official databases **Chebi** and **UniProt** to gather metadata. For more examples, please visit our [documentation](https://pyenzyme.readthedocs.io/en/latest/index.html#) (Work in progress)
+This example will demonstrate how to create a simple EnzymeML document using PyEnzyme and how to use initializers from
+official databases **Chebi** and **UniProt** to gather metadata. For more examples, please visit
+our [documentation](https://pyenzyme.readthedocs.io/en/latest/index.html#) (Work in progress)
 
 ```python
-import pyenzyme as pe
-
-# Initialize your document
-enzmldoc = pe.EnzymeMLDocument(name="MyDoc")
-
-# Create a vessel and add it to the document
-vessel = pe.Vessel(name="Falcon Tube", volume=10.0, unit="ml")
-vessel_id = enzmldoc.addVessel(vessel)
-
-# Set up reactants and proteins from databases
-protein = pe.Protein.fromUniProtID(
-    uniprotid="P07327", vessel_id=vessel_id,
-    init_conc=10.0, unit="fmole / l"
-)
-
-substrate = pe.Reactant.fromChebiID(
-    chebi_id="CHEBI:16236", vessel_id=vessel_id,
-    init_conc=200.0, unit="mmole / l"
-) 
-
-product = pe.Reactant.fromChebiID(
-    chebi_id="CHEBI:15343", vessel_id=vessel_id,
-    init_conc=0.0, unit="mmole / l"
-)
-
-# ... and add each to the document
-protein_id = enzmldoc.addProtein(protein)
-substrate_id = enzmldoc.addReactant(substrate)
-product_id = enzmldoc.addReactant(product)
-
-# Build the reaction
-reaction = pe.EnzymeReaction.fromEquation(
-    equation="ethanol -> acetaldehyde",
-    modifiers=[protein_id],
-    name="Alocohol dehydrogenation",
-    enzmldoc=enzmldoc
-)
-
-# ... and add it to the document
-reaction_id = enzmldoc.addReaction(reaction)
-
-# Finally, save the document to an OMEX archive
-enzmldoc.toFile(".", name="ADH Experiment")
+# To be added for V2
 ```
+
 <sub>(Code should run as it is)</sup>
 
 ## 📖 Documentation and more examples
 
-Explore all the features of **PyEnzyme** in our [documentation](https://pyenzyme.readthedocs.io/en/latest/index.html#) and take part in [Discussions](https://github.com/EnzymeML/PyEnzyme/discussions) and/or [Issues](https://github.com/EnzymeML/PyEnzyme/issues). 
+Explore all the features of **PyEnzyme** in our [documentation](https://pyenzyme.readthedocs.io/en/latest/index.html#)
+and take part in [Discussions](https://github.com/EnzymeML/PyEnzyme/discussions)
+and/or [Issues](https://github.com/EnzymeML/PyEnzyme/issues).
+
+## 🧪 Testing
+
+In order to run tests there are two different ways. First you can utilize `pytest` directly by running the following:
+
+```bash
+python -m pytest -vv
+```
+
+Or you can the provided Dockerfile to run the tests in a containerized environment.
+
+```bash
+docker build -t pyenzyme .
+docker run pyenzyme
+```
 
 ## ⚠️ License
 
-`PyEnzyme` is free and open-source software licensed under the [BSD 2-Clause License](https://github.com/EnzymeML/PyEnzyme/blob/main/LICENSE). 
+`PyEnzyme` is free and open-source software licensed under
+the [BSD 2-Clause License](https://github.com/EnzymeML/PyEnzyme/blob/main/LICENSE).

dev-examples/Readme.md

@@ -0,0 +1,12 @@
+# Dev Examples
+
+These examples are intended to be used during development towards 2.0.0 and will be removed in the final release.
+
+## How to run the examples
+
+Dev examples should be run from the root directory of the repository and will produce outputs to the dev-example folder.
+
+```bash
+# From the root directory
+python ./dev-examples/*.py
+```