pymodrev 0.1.0__tar.gz

pymodrev-0.1.0/.github/workflows/python-publish.yml

@@ -0,0 +1,36 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - 'v*' # Trigger workflow on tags that start with "v" (e.g., v1.0.0)
+
+jobs:
+  build-and-publish:
+    name: Build and publish to PyPI
+    runs-on: ubuntu-latest
+    
+    # Required for trusted publishing to PyPI
+    permissions:
+      id-token: write
+      contents: read
+
+    steps:
+    - name: Checkout Code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # Important for setuptools_scm to get the full git history and tags
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - name: Install build dependencies
+      run: python -m pip install --upgrade pip build
+
+    - name: Build sdist and wheel
+      run: python -m build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

pymodrev-0.1.0/.gitignore

@@ -0,0 +1,10 @@
+__pycache__
+.DS_Store
+.vscode
+venv
+build
+ModRev
+pyfunctionhood
+bin
+GINsim-data
+*.egg-info/

pymodrev-0.1.0/CHANGELOG.md

@@ -0,0 +1,37 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+---
+
+## v1.0 - Feb 2026
+
+### Added
+- Added `.csv` format support as a proposal for observation files.
+- Option to write and export repaired model files under a new unified parser module.
+- Full `model.zginml` support with unified parsing of Boolean expressions.
+- Added `vertex` node support.
+- Fully functioning `asp_reader` with example files and `pytest` integration.
+- Replaced custom shell test scripts (`run_tests.sh`) with native `pytest` testing (`test_model_files.py`).
+- Extensively populated the `examples/` directory for test automation.
+- Introduced a standard logging system, including a specific debug mode for updaters.
+- Support for multiple observation files of the same topology in a single run.
+
+### Changed
+- Readers have been redesigned as polymorphic **Parsers** (`parser_ginml.py`, `parser_bnet.py`, `parser_asp.py`), capable of both `read()` and `write()` operations.
+- The **BNET** parser now evaluates functions comprehensively using Quine-McCluskey logic reduction, dropping degenerate regulators, and assuming monotonicity (defaulting to positive).
+- Repaired `GINsim` networks now retain their original `.ginml` XML layout styling and preserve the inner files of `.zginml` zip archives.
+- Edge signs are explicitly displayed in function repair proposals.
+- Significant refactoring of the repair engine, and simplified dynamic loading of updater classes.
+- Changed configuration class structures, now utilizing elegant pythonic `@property` getters and setters.
+- Migrated all command-line interface arguments to `argparse`.
+- Cleaned up unneeded dependencies such as `asp_helper` and consolidated the code.
+
+### Fixed
+- Fixed node order sorting in multiple `.lp` model test files.
+- Resolved severe syntax errors causing invalid `JSON` outputs.
+
+---
+
+## v0.x - Feb 2025
+- First base stable release with consistency check and repair operations

pymodrev-0.1.0/PKG-INFO

@@ -0,0 +1,156 @@
+Metadata-Version: 2.4
+Name: pymodrev
+Version: 0.1.0
+Summary: Model Revision tool for computing Boolean network repair operations.
+Author-email: "Pedro T. Monteiro" <Pedro.Tiago.Monteiro@tecnico.ulisboa.pt>
+License: MIT
+Project-URL: Homepage, https://github.com/ptgm/pymodrev
+Project-URL: Repository, https://github.com/ptgm/pymodrev
+Keywords: boolean,revision,repair,network,function
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: GNU Affero General Public License v3
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Libraries
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Requires-Dist: bitarray
+Requires-Dist: pyfunctionhood
+Requires-Dist: clingo
+
+## pymodrev: A python Model Revision tool for Boolean logical models
+
+**pymodrev** is a Python-based reimplementation of [ModRev](https://github.com/FilipeGouveia/ModRev), a tool for automated **consistency checking** and **repair** of Boolean network models using **Answer Set Programming (ASP)**. Given a Boolean model and a set of experimental observations (steady-state or time-series), pymodrev determines whether the model explains the data. If inconsistencies are found, it identifies **minimal repair operations** to fix the model.
+
+Built on top of the [Clingo](https://potassco.org/clingo/) ASP solver and the [`pyfunctionhood`](https://github.com/ptgm/pyfunctionhood) library, pymodrev brings modern usability and extensibility to the model revision process by offering:
+
+* ✅ **Full parity with [ModRev](https://filipegouveia.github.io/ModRev/)'s core logic**, using the same ASP encodings
+* ✅ **Modular architecture** with pluggable update policies (synchronous, asynchronous, complete, steady-state)
+* ✅ **Pure Python interface**, ideal for integration with scientific workflows
+* ✅ **In-memory model and observation management**, enabling multiple consistency checks without reloading
+* ✅ **Command-line interface** for batch processing and reproducibility
+
+---
+### Install
+
+You can install **pymodrev** directly from source or via PyPI.
+
+To install from source (when you are inside the pymodrev directory):
+```bash
+$ pip install .
+```
+
+To install from PyPI:
+```bash
+$ pip install pymodrev
+```
+
+This will automatically install dependencies like `bitarray`, `pyfunctionhood`, and `clingo`.
+
+---
+
+### Getting Started
+
+Boolean models can be specified using the following formats:
+
+* `.lp` - using original [ModRev](https://filipegouveia.github.io/ModRev/) ASP encoding
+* `.bnet` - using the BoolNet format (only boolean rules)
+* `.ginml` / `.zginml` - using the widely used GINsim format (conserving the model layout information)
+
+To run **pymodrev**, use the following command structure:
+
+```bash
+$ pymodrev -h
+```
+```bash
+usage: pymodrev [-h] -m MODEL -obs OBS [UPDATER ...] -t {c,r,m} [--exhaustive-search] [--sub-opt] [--all-opt]
+               [-v {0,1,2}] [-d]
+
+options:
+  -h, --help            show this help message and exit
+  -m, --model MODEL     Input model file.
+  -obs, --observations OBS [UPDATER ...]
+                        List of observation files and updater pairs.
+                        Each observation must be followed by its updater type. 
+                        Example: -obs obs1.lp asyncupdater obs2.lp syncupdater
+  -t, --task {c,r,m}    Specify the task to perform (default=r):
+                           c - check for consistency
+                           r - get repairs
+                           m - get repaired models
+  --exhaustive-search   Force exhaustive search of function repair operations (default=false).
+  --sub-opt             Show sub-optimal solutions found (default=false).
+  --all-opt             Computes all optimal solutions (default=true).
+                        Stops at first optimal solution if false.
+  -v, --verbose {0,1,2}
+                        Specify output verbose level (default=2):
+                            0 - compact format
+                            1 - json format
+                            2 - human-readable format
+  -d, --debug           Enable debug mode.
+```
+
+
+#### Example: check consistency
+
+Using option `-t c`, `pymodrev` will report the minimal set of nodes that need to be repaired in order to make the model consistent with the given observations.
+
+```bash
+$ pymodrev -m examples/boolean_cell_cycle/03/model.bnet -obs examples/boolean_cell_cycle/03/steadystate.lp steadystateupdater -t c
+```
+```bash
+This network is inconsistent!
+  node(s) needing repair: "p27", "rb", "cdc20", "cycd"
+  present in profile(s): "p1"
+```
+
+#### Example: get repairs
+
+Using option `-t r`, `pymodrev` will report the minimal set of repair operations for the model to be consistent with the given observations.
+
+```bash
+$ pymodrev -m examples/boolean_cell_cycle/03/model.bnet -obs examples/boolean_cell_cycle/03/steadystate.lp steadystateupdater -t r
+```
+```bash
+### Found solution with 4 repair operations.
+	Inconsistent node p27.
+		Repair #1:
+			Change function of p27 to: (cyca && !cycb && cycd && !p27) || (!cycb && !cyce)
+	Inconsistent node rb.
+		Repair #1:
+			Change function of rb to: (!cycb && cycd && !p27) || (!cycb && cycd && cyce) || (!cycb && !cyca)
+	Inconsistent node cdc20.
+		Repair #1:
+			Flip sign of edge (cycb,cdc20) to: positive
+	Inconsistent node cycd.
+		Repair #1:
+			Flip sign of edge (cycd,cycd) to: positive
+```
+
+#### Example: get repaired models
+
+Using option `-t m`, `pymodrev` will apply the repairs to the model and write to disk the repaired models consistent with the given observations.
+
+```bash
+$ pymodrev -m examples/boolean_cell_cycle/03/model.bnet -obs examples/boolean_cell_cycle/03/steadystate.lp steadystateupdater -t m
+```
+Repaired models keep the original name followed by a number, representing the number of minimal alternative repairs.
+For example, one could have:
+
+* `model_1.bnet ... model_2.bnet`, if there were only two possible minimal repaired models.
+* `model_01.bnet ... model_18.bnet`, if there were eighteen possible minimal repaired models.
+
+---
+
+### Authors
+* Filipe Gouveia ([https://github.com/FilipeGouveia](https://github.com/FilipeGouveia))
+* Antonio Romeu ([https://github.com/antonioromeu](https://github.com/antonioromeu))
+* Pedro T. Monteiro ([https://github.com/ptgm](https://github.com/ptgm))

pymodrev-0.1.0/README.md

@@ -0,0 +1,127 @@
+## pymodrev: A python Model Revision tool for Boolean logical models
+
+**pymodrev** is a Python-based reimplementation of [ModRev](https://github.com/FilipeGouveia/ModRev), a tool for automated **consistency checking** and **repair** of Boolean network models using **Answer Set Programming (ASP)**. Given a Boolean model and a set of experimental observations (steady-state or time-series), pymodrev determines whether the model explains the data. If inconsistencies are found, it identifies **minimal repair operations** to fix the model.
+
+Built on top of the [Clingo](https://potassco.org/clingo/) ASP solver and the [`pyfunctionhood`](https://github.com/ptgm/pyfunctionhood) library, pymodrev brings modern usability and extensibility to the model revision process by offering:
+
+* ✅ **Full parity with [ModRev](https://filipegouveia.github.io/ModRev/)'s core logic**, using the same ASP encodings
+* ✅ **Modular architecture** with pluggable update policies (synchronous, asynchronous, complete, steady-state)
+* ✅ **Pure Python interface**, ideal for integration with scientific workflows
+* ✅ **In-memory model and observation management**, enabling multiple consistency checks without reloading
+* ✅ **Command-line interface** for batch processing and reproducibility
+
+---
+### Install
+
+You can install **pymodrev** directly from source or via PyPI.
+
+To install from source (when you are inside the pymodrev directory):
+```bash
+$ pip install .
+```
+
+To install from PyPI:
+```bash
+$ pip install pymodrev
+```
+
+This will automatically install dependencies like `bitarray`, `pyfunctionhood`, and `clingo`.
+
+---
+
+### Getting Started
+
+Boolean models can be specified using the following formats:
+
+* `.lp` - using original [ModRev](https://filipegouveia.github.io/ModRev/) ASP encoding
+* `.bnet` - using the BoolNet format (only boolean rules)
+* `.ginml` / `.zginml` - using the widely used GINsim format (conserving the model layout information)
+
+To run **pymodrev**, use the following command structure:
+
+```bash
+$ pymodrev -h
+```
+```bash
+usage: pymodrev [-h] -m MODEL -obs OBS [UPDATER ...] -t {c,r,m} [--exhaustive-search] [--sub-opt] [--all-opt]
+               [-v {0,1,2}] [-d]
+
+options:
+  -h, --help            show this help message and exit
+  -m, --model MODEL     Input model file.
+  -obs, --observations OBS [UPDATER ...]
+                        List of observation files and updater pairs.
+                        Each observation must be followed by its updater type. 
+                        Example: -obs obs1.lp asyncupdater obs2.lp syncupdater
+  -t, --task {c,r,m}    Specify the task to perform (default=r):
+                           c - check for consistency
+                           r - get repairs
+                           m - get repaired models
+  --exhaustive-search   Force exhaustive search of function repair operations (default=false).
+  --sub-opt             Show sub-optimal solutions found (default=false).
+  --all-opt             Computes all optimal solutions (default=true).
+                        Stops at first optimal solution if false.
+  -v, --verbose {0,1,2}
+                        Specify output verbose level (default=2):
+                            0 - compact format
+                            1 - json format
+                            2 - human-readable format
+  -d, --debug           Enable debug mode.
+```
+
+
+#### Example: check consistency
+
+Using option `-t c`, `pymodrev` will report the minimal set of nodes that need to be repaired in order to make the model consistent with the given observations.
+
+```bash
+$ pymodrev -m examples/boolean_cell_cycle/03/model.bnet -obs examples/boolean_cell_cycle/03/steadystate.lp steadystateupdater -t c
+```
+```bash
+This network is inconsistent!
+  node(s) needing repair: "p27", "rb", "cdc20", "cycd"
+  present in profile(s): "p1"
+```
+
+#### Example: get repairs
+
+Using option `-t r`, `pymodrev` will report the minimal set of repair operations for the model to be consistent with the given observations.
+
+```bash
+$ pymodrev -m examples/boolean_cell_cycle/03/model.bnet -obs examples/boolean_cell_cycle/03/steadystate.lp steadystateupdater -t r
+```
+```bash
+### Found solution with 4 repair operations.
+	Inconsistent node p27.
+		Repair #1:
+			Change function of p27 to: (cyca && !cycb && cycd && !p27) || (!cycb && !cyce)
+	Inconsistent node rb.
+		Repair #1:
+			Change function of rb to: (!cycb && cycd && !p27) || (!cycb && cycd && cyce) || (!cycb && !cyca)
+	Inconsistent node cdc20.
+		Repair #1:
+			Flip sign of edge (cycb,cdc20) to: positive
+	Inconsistent node cycd.
+		Repair #1:
+			Flip sign of edge (cycd,cycd) to: positive
+```
+
+#### Example: get repaired models
+
+Using option `-t m`, `pymodrev` will apply the repairs to the model and write to disk the repaired models consistent with the given observations.
+
+```bash
+$ pymodrev -m examples/boolean_cell_cycle/03/model.bnet -obs examples/boolean_cell_cycle/03/steadystate.lp steadystateupdater -t m
+```
+Repaired models keep the original name followed by a number, representing the number of minimal alternative repairs.
+For example, one could have:
+
+* `model_1.bnet ... model_2.bnet`, if there were only two possible minimal repaired models.
+* `model_01.bnet ... model_18.bnet`, if there were eighteen possible minimal repaired models.
+
+---
+
+### Authors
+* Filipe Gouveia ([https://github.com/FilipeGouveia](https://github.com/FilipeGouveia))
+* Antonio Romeu ([https://github.com/antonioromeu](https://github.com/antonioromeu))
+* Pedro T. Monteiro ([https://github.com/ptgm](https://github.com/ptgm))

pymodrev-0.1.0/examples/boolean_cell_cycle/00/README

@@ -0,0 +1,2 @@
+boolean_cell_cycle/original/boolean_cell_cycle.lp
+boolean_cell_cycle/original/attractors.lp with obs_vlabel(p1,cycb,0).

pymodrev-0.1.0/examples/boolean_cell_cycle/00/model.bnet

@@ -0,0 +1,11 @@
+targets, factors
+cycb, !cdc20 & !cdh1
+cdc20, cycb
+cdh1, !cyca & !cycb | !cycb & p27 | cdc20
+rb, !cycd & !cyce & !cyca & !cycb | !cycd & p27 & !cycb
+cyca, !rb & cyca & !cdc20 & !cdh1 | !rb & cyca & !cdc20 & !ubch10 | !rb & e2f & !cdc20 & !cdh1 | !rb & e2f & !cdc20 & !ubch10
+ubch10, cdc20 & ubch10 | cycb & ubch10 | cyca & ubch10 | !cdh1
+e2f, !rb & !cyca & !cycb | !rb & p27 & !cycb
+cycd, cycd
+cyce, !rb & e2f
+p27, !cycd & !cyce & !cyca & !cycb | !cycd & !cyca & p27 & !cycb | !cycd & !cyce & p27 & !cycb

pymodrev-0.1.0/examples/boolean_cell_cycle/00/model.lp

@@ -0,0 +1,136 @@
+vertex(cyca).
+vertex(rb).
+vertex(cycb).
+vertex(cdc20).
+vertex(cdh1).
+vertex(cycd).
+vertex(cyce).
+vertex(e2f).
+vertex(p27).
+vertex(ubch10).
+
+edge(cycb, cdc20, 1).
+edge(cdh1, cdc20, 1).
+
+functionOr(cdc20, 1).
+functionAnd(cdc20, 1, cycb).
+
+edge(rb, cyca, 0).
+edge(cyca, cyca, 1).
+edge(cdc20, cyca, 0).
+edge(cdh1, cyca, 0).
+edge(ubch10, cyca, 0).
+edge(e2f, cyca, 1).
+
+functionOr(cyca, 1..4).
+functionAnd(cyca, 1, rb).
+functionAnd(cyca, 1, cyca).
+functionAnd(cyca, 1, cdc20).
+functionAnd(cyca, 1, cdh1).
+functionAnd(cyca, 2, rb).
+functionAnd(cyca, 2, cyca).
+functionAnd(cyca, 2, cdc20).
+functionAnd(cyca, 2, ubch10).
+functionAnd(cyca, 3, rb).
+functionAnd(cyca, 3, e2f).
+functionAnd(cyca, 3, cdc20).
+functionAnd(cyca, 3, cdh1).
+functionAnd(cyca, 4, rb).
+functionAnd(cyca, 4, e2f).
+functionAnd(cyca, 4, cdc20).
+functionAnd(cyca, 4, ubch10).
+
+edge(cdc20, cycb, 0).
+edge(cdh1, cycb, 0).
+
+functionOr(cycb, 1).
+functionAnd(cycb, 1, cdc20).
+functionAnd(cycb, 1, cdh1).
+
+edge(cycd, cycd, 1).
+
+functionOr(cycd, 1).
+functionAnd(cycd, 1, cycd).
+
+edge(rb, cyce, 0).
+edge(e2f, cyce, 1).
+
+functionOr(cyce, 1).
+functionAnd(cyce, 1, rb).
+functionAnd(cyce, 1, e2f).
+
+edge(rb, e2f, 0).
+edge(cyca, e2f, 0).
+edge(cycb, e2f, 0).
+edge(p27, e2f, 1).
+
+functionOr(e2f, 1..2).
+functionAnd(e2f, 1, rb).
+functionAnd(e2f, 1, cyca).
+functionAnd(e2f, 1, cycb).
+functionAnd(e2f, 2, rb).
+functionAnd(e2f, 2, p27).
+functionAnd(e2f, 2, cycb).
+
+edge(cycd, rb, 0).
+edge(cyce, rb, 0).
+edge(cyca, rb, 0).
+edge(cycb, rb, 0).
+edge(p27, rb, 1).
+
+functionOr(rb, 1..2).
+functionAnd(rb, 1, cycd).
+functionAnd(rb, 1, cyce).
+functionAnd(rb, 1, cyca).
+functionAnd(rb, 1, cycb).
+functionAnd(rb, 2, cycd).
+functionAnd(rb, 2, p27).
+functionAnd(rb, 2, cycb).
+
+edge(cdc20, ubch10, 1).
+edge(ubch10, ubch10, 1).
+edge(cycb, ubch10, 1).
+edge(cyca, ubch10, 1).
+edge(cdh1, ubch10, 0).
+
+functionOr(ubch10, 1..4).
+functionAnd(ubch10, 1, cdc20).
+functionAnd(ubch10, 1, ubch10).
+functionAnd(ubch10, 2, cycb).
+functionAnd(ubch10, 2, ubch10).
+functionAnd(ubch10, 3, cyca).
+functionAnd(ubch10, 3, ubch10).
+functionAnd(ubch10, 4, cdh1).
+
+edge(cyca, cdh1, 0).
+edge(cycb, cdh1, 0).
+edge(p27, cdh1, 1).
+edge(cdc20, cdh1, 1).
+
+functionOr(cdh1, 1..3).
+functionAnd(cdh1, 1, cyca).
+functionAnd(cdh1, 1, cycb).
+functionAnd(cdh1, 2, cycb).
+functionAnd(cdh1, 2, p27).
+functionAnd(cdh1, 3, cdc20).
+
+edge(cycd, p27, 0).
+edge(cyce, p27, 0).
+edge(cyca, p27, 0).
+edge(cycb, p27, 0).
+edge(p27, p27, 1).
+
+functionOr(p27, 1..3).
+functionAnd(p27, 1, cycd).
+functionAnd(p27, 1, cyce).
+functionAnd(p27, 1, cyca).
+functionAnd(p27, 1, cycb).
+functionAnd(p27, 2, cycd).
+functionAnd(p27, 2, cyca).
+functionAnd(p27, 2, p27).
+functionAnd(p27, 2, cycb).
+functionAnd(p27, 3, cycd).
+functionAnd(p27, 3, cyce).
+functionAnd(p27, 3, p27).
+functionAnd(p27, 3, cycb).
+

pymodrev-0.1.0/examples/boolean_cell_cycle/00/output.txt

@@ -0,0 +1 @@
+Consistent!

pymodrev-0.1.0/examples/boolean_cell_cycle/00/steadystate.csv

@@ -0,0 +1,2 @@
+,cycb,cyca,cdc20,ubch10,cycd,p27,cyce,rb,cdh1,e2f
+p1,0,0,0,0,0,1,0,1,1,0

pymodrev-0.1.0/examples/boolean_cell_cycle/00/steadystate.lp

@@ -0,0 +1,11 @@
+exp(p1).
+obs_vlabel(p1,cycb,0).
+obs_vlabel(p1,cyca,0).
+obs_vlabel(p1,cdc20,0).
+obs_vlabel(p1,ubch10,0).
+obs_vlabel(p1,cycd,0).
+obs_vlabel(p1,p27,1).
+obs_vlabel(p1,cyce,0).
+obs_vlabel(p1,rb,1).
+obs_vlabel(p1,cdh1,1).
+obs_vlabel(p1,e2f,0).

pymodrev-0.1.0/examples/boolean_cell_cycle/01/README

@@ -0,0 +1,2 @@
+boolean_cell_cycle/original/boolean_cell_cycle.lp
+boolean_cell_cycle/original/attractors.lp with obs_vlabel(p1,cycb,0).

pymodrev-0.1.0/examples/boolean_cell_cycle/01/model.bnet

@@ -0,0 +1,11 @@
+targets, factors
+cycb, !cdc20 & !cdh1
+cdc20, cycb
+cdh1, !cyca & !cycb | !cycb & p27 | cdc20
+rb, !cycd & !cyce & !cyca & !cycb | !cycd & p27 & !cycb
+cyca, !rb & cyca & !cdc20 & !cdh1 | !rb & cyca & !cdc20 & !ubch10 | !rb & e2f & !cdc20 & !cdh1 | !rb & e2f & !cdc20 & !ubch10
+ubch10, cdc20 & ubch10 | cycb & ubch10 | cyca & ubch10 | !cdh1
+e2f, !rb & !cyca & !cycb | !rb & p27 & !cycb
+cycd, cycd
+cyce, !rb & e2f
+p27, !cycd & !cyce & !cyca & !cycb | !cycd & !cyca & p27 & !cycb | !cycd & !cyce & p27 & !cycb