Skip to content

Commit 34bfb32

Browse files
longxf21longxf21
committed
Docs update
1 parent ed1a3d7 commit 34bfb32

File tree

4 files changed

+114
-31
lines changed

4 files changed

+114
-31
lines changed

‎.github/workflows/update-changelog.yml

+35
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
name: Update Changelog
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
workflow_dispatch:
8+
9+
jobs:
10+
update-changelog:
11+
runs-on: ubuntu-latest
12+
13+
steps:
14+
- name: Checkout repository
15+
uses: actions/checkout@v3
16+
with:
17+
fetch-depth: 0 # Fetch full history for changelog generation
18+
19+
- name: Install dependencies (for git-cliff)
20+
run: |
21+
sudo apt update
22+
sudo apt install -y cargo
23+
cargo install git-cliff
24+
25+
- name: Generate Changelog
26+
run: |
27+
git-cliff -o CHANGELOG.md
28+
29+
- name: Commit and Push Changes
30+
run: |
31+
git config --global user.name "github-actions[bot]"
32+
git config --global user.email "github-actions[bot]@users.noreply.github.com"
33+
git add CHANGELOG.md
34+
git commit -m "chore: update changelog [skip ci]" || echo "No changes to commit"
35+
git push origin main || echo "No changes to push"

‎Changelog.md

+51
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,51 @@
1+
# Changelog
2+
3+
All notable changes to this project will be documented in this file.
4+
5+
## [0.2.7] - Latest
6+
- Documentation improvements
7+
8+
## [0.2.6] - Previous
9+
- Created ReadTheDocs
10+
- Bug fixes
11+
- Improved test coverage to 99%
12+
13+
## [0.2.5]
14+
- Separated model reading from analysis
15+
- Tested on 1054 biomodels and fixed bugs
16+
- Added check_model method to allow users to use the package with one line
17+
- Solved issue with running sympy with built-in symbols such as "S"
18+
19+
## [0.2.4]
20+
- Updated instructions in README
21+
22+
## [0.2.3]
23+
- Included .json files
24+
- Fixed path finding issue
25+
26+
## [0.2.2]
27+
- Bug fixes
28+
- Created GitHub workflow for CI
29+
30+
## [0.2.1]
31+
- Removed Analyzer.check()
32+
- Added get_all_checks() to get info about all checks
33+
- Improved testing to full coverage except for trivial ones
34+
- Improved exception messages
35+
- Allowed string of Antimony or SBML model as input
36+
- Simplified the import statement
37+
- Revised existing and added new method and class comments
38+
39+
## [0.2.0]
40+
- Removed numpy dependency
41+
- Updated rate law classification scheme
42+
- No longer using SBMLKinetics for rate law classifications
43+
- Restructured code for web integration
44+
45+
## [0.1.0]
46+
- Initial release
47+
- Used SBMLKinetics for rate law classifications
48+
49+
---
50+
51+
For the latest release notes, check the [GitHub Releases](https://github.com/sys-bio/ratesb_python/releases).

‎README.md

+18-31
Original file line numberDiff line numberDiff line change
@@ -20,10 +20,20 @@ Below are examples demonstrating how to use the ratesb_python package with file
2020

2121
Simple example:
2222
```python
23-
from ratesn_python import check_model
23+
from ratesb_python import check_model
2424
print(check_model("S->P;k1*S"))
2525
```
2626

27+
Expected output:
28+
```bash
29+
_J0:
30+
Warning 1004: Flux is not decreasing as product increases.
31+
```
32+
33+
Explanation:
34+
- `_J0` represents an internal identifier for the reaction flux. It is automatically assigned to the reaction for tracking purposes.
35+
- The warning (1004) indicates that as the product (P) increases, the flux does not decrease as expected, suggesting a potential issue with the reversible reaction kinetics.
36+
2737
Complex example:
2838
```python
2939
from ratesb_python import Analyzer
@@ -172,44 +182,21 @@ python -m unittest
172182

173183
## Release Notes
174184

175-
### 0.1.0
176-
* initial release, used SBMLKinetics for rate law classifications
177-
178-
### 0.2.0
179-
* removed numpy dependency
180-
* updated rate law classifications scheme, no longer using SBMLKinetics for rate law classifications
181-
* Restructured code for web integration
182-
183-
### 0.2.1
184-
* removed Analyzer.check()
185-
* added get_all_checks() to get the info about all checks
186-
* improved testing to full coverage except for trivial ones
187-
* improved exception messages
188-
* allowed string of Antimony or SBML model as input
189-
* simplified the import statement
190-
* revised existing and added new method and class comments
191-
192-
### 0.2.2
193-
* bug fixes
194-
* created github workflow for CI
195-
196-
### 0.2.3
197-
* include .json files
198-
* fixed path finding issue
185+
### 0.2.7
186+
* Doc improvements
199187

200-
### 0.2.4
201-
* updated instructions in readme
188+
### 0.2.6
189+
* Created ReadTheDocs
190+
* Bug Fixes
191+
* Improved test coverage to 99%
202192

203193
### 0.2.5
204194
* Separated model reading from analysis
205195
* Tested on 1054 biomodels and fixed bugs
206196
* Added check_model method to allow user to use the package with one line
207197
* Solved when running sympy with sympy builtin symbols that raise error such as "S", a reaction like "S->P;k1*S" would work now
208198

209-
### 0.2.6
210-
* Created ReadTheDocs
211-
* Bug Fixes
212-
* Improved test coverage to 99%
199+
For older versions and a full changelog, please check the repository's [Changelog.md](https://github.com/sys-bio/ratesb_python/blob/main/Changelog.md).
213200

214201
## Contributing
215202

‎docs/source/installation.rst

+10
Original file line numberDiff line numberDiff line change
@@ -6,3 +6,13 @@ To install `ratesb_python`, execute the following command in your terminal:
66
.. code-block:: bash
77
88
pip install ratesb_python
9+
10+
Dependencies
11+
------------
12+
13+
The following dependencies are required and will be installed automatically. However, if you need version-specific details, refer to the `pyproject.toml` file or use `pip show <package>` after installation.
14+
15+
- `antimony`
16+
- `sbmlkinetics`
17+
- `sympy`
18+
- `python-libsbml`

0 commit comments

Comments
 (0)