PyAntiGen 1.0.4__tar.gz → 1.0.7__tar.gz

{pyantigen-1.0.4 → pyantigen-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyAntiGen
-Version: 1.0.4
+Version: 1.0.7
 Summary: Short one-line description of what PyAntiGen does
 Author: Open Source Contributor
 Author-email: Don <you@example.com>
@@ -36,8 +36,12 @@ PyAntiGen is a declarative, object-oriented framework for generating compartment
 - **Isotope Tracking:** Natively supports tracking labeled isotopes and generating corresponding parallel reactions.
 
 ## Installation
+You can install PyAntiGen into your Python environment with:
+```bash
+pip install pyantigen
+```
 
-You can install PyAntiGen globally into your preferred Python environment by cloning this repository and running pip:
+You can also install PyAntiGen globally into your preferred Python environment by cloning this repository and running pip:
 
 ```bash
 git clone https://github.com/elbert5770/PyAntiGen.git
@@ -49,7 +53,7 @@ pip install -e .
 
 Because PyAntiGen is installed as a system-level Python package, you don't need a copy of the framework files in your working directory. 
 
-To start a brand new modeling workspace, just open a terminal and navigate to a folder where you want it to live (not PyAntiGen) and run:
+To start a brand new modeling workspace, just open a terminal and navigate to a folder where you want your project to live (be careful not to build within the PyAntiGen folder itself) and run:
 
 ```bash
 pyantigen-create MyNewModel
@@ -60,18 +64,16 @@ This will automatically scaffold the following project directory:
 MyNewModel/
 ├── .agents/
 │   └── skills/          (agent skills, e.g. module generation, ODE conversion)
-├── scripts/
-│   ├── Example/         (full example: generate, run, optimize + Modules/)
-│   │   ├── Example_generate.py
-│   │   ├── Example_run.py
-│   │   ├── Example_optimize.py
+├── Projects/
+│   ├── Example/         (full example: generate, run + Modules/, Engine/)
+│   │   ├── Model_generate.py
+│   │   ├── Model_run.py
 │   │   └── Modules/     (Data, AntimonyGen, Plots, Simulate, Optimize, Experiment, Events)
-│   └── MyNewModel/      (same structure, Modules/ left empty for your code)
-│       ├── MyNewModel_generate.py
-│       ├── MyNewModel_run.py
-│       ├── MyNewModel_optimize.py
+│   └── MyNewModel/      (same structure, Modules/ pre-populated from Example)
+│       ├── Model_generate.py
+│       ├── Model_run.py
 │       └── Modules/     (Data, AntimonyGen, Plots, Simulate, Optimize, Experiment, Events)
-├── modules/
+├── antimony_modules/
 │   └── __init__.py      (plus Basic/ for the example)
 ├── data/                (Example experiment CSVs copied for the example)
 ├── antimony_models/
@@ -79,36 +81,41 @@ MyNewModel/
 ├── generated/
 │   └── Example/         (reaction dict, rules, etc. after generate)
 ├── results/
-│   └── Example/         (plots from Example_run.py)
+│   └── Example/         (plots from Model_run.py)
 ├── SBML_models/
 └── pyantigen_settings.json   (e.g. archive_with_timestamp: false)
 ```
 
-All model-specific files are grouped under folders named by `MODEL_NAME` (e.g. `Example` or your project name). From `MyNewModel/scripts/Example/` run:
+Every project folder under `Projects/` has a script called `Model_generate.py` that is run to generate the model. `MODEL_NAME` is derived automatically from the enclosing folder name (see `AntiGen_paths.py`), so being in the right project folder is all that's needed to generate/run the correct project. From `MyNewModel/Projects/Example/` run:
 
 ```bash
-python Example_generate.py
+python Model_generate.py
 ```
 
-This generates the model and writes outputs to `antimony_models/Example/` and `generated/Example/`. Edit parameters if desired in `antimony_models/Example/Example_parameters.csv`, then run:
+This generates the model from the specified files in 'antimony_modules' and writes outputs to `antimony_models/Example/` and `generated/Example/`. This is entirely optional as Model_run.py also calls the constructor functions in `Model_generate.py`.
+
+To run a simulation or optimization, you may edit the parameters in `antimony_models/Example/Example_parameters.csv`, derived parameters in `antimony_models/Example/Example_manual.txt`, and initial conditions in `antimony_models/Example/Example_InitialConditions.csv`.
+
+Then, run `Model_run.py` to simulate the Example in Tellurium/RoadRunner:
 
 ```bash
-python Example_run.py
+python Model_run.py --simulate Example
 ```
 
-For parameter fitting against data, run:
+To run optimization examples use the --optimize flag:
 
 ```bash
-python Example_optimize.py
+python Model_run.py --optimize Example1
+python Model_run.py --optimize Example2
+python Model_run.py --optimize Example3
 ```
 
-Your own model lives under `scripts/MyNewModel/` with the same files as the Example. Modify the code for your model in `scripts/MyNewModel/Modules/` and `scripts/MyNewModel/MyNewModel_generate.py`, `scripts/MyNewModel/MyNewModel_run.py`, and `scripts/MyNewModel/MyNewModel_optimize.py'. Your problem will also require new modules in folder 'modules'.
+Your own model lives under `Projects/MyNewModel/`. Modify the code for your model in `Projects/MyNewModel/Modules/`, `Projects/MyNewModel/Model_generate.py`, and `Projects/MyNewModel/Model_run.py`. Your problem will also require new modules in `antimony_modules/` to define the model.
 
-Keeping the generation and simulation steps separate gives you time to adjust parameters and inspect the generated files before running.
 
 ### Running from an IDE (Cursor / VS Code)
 
 The **Play** button uses whichever Python interpreter is currently selected. If your environment (conda/venv) isn’t loaded, the run may fail with import or path errors.
 
 1. **Select the correct interpreter**: `Ctrl+Shift+P` (or `Cmd+Shift+P` on macOS) → **Python: Select Interpreter** → choose the environment where you ran `pip install -e .` (e.g. your conda or venv).
-2. **Run from project root**: Open the *project* folder (e.g. `MyNewModel`) as the workspace. Use **Run and Debug** (or Play on `scripts/Example/Example_run.py`); the project root is resolved from the script location so `antimony_models/Example/`, `generated/Example/`, and `results/Example/` resolve correctly.
+2. **Run from project root**: Open the *project* folder (e.g. `MyNewModel`) as the workspace. Use **Run and Debug** (or Play on `Projects/Example/Model_run.py`); the project root is resolved from the script location so `antimony_models/Example/`, `generated/Example/`, and `results/Example/` resolve correctly.

{pyantigen-1.0.4 → pyantigen-1.0.7}/PyAntiGen.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyAntiGen
-Version: 1.0.4
+Version: 1.0.7
 Summary: Short one-line description of what PyAntiGen does
 Author: Open Source Contributor
 Author-email: Don <you@example.com>
@@ -36,8 +36,12 @@ PyAntiGen is a declarative, object-oriented framework for generating compartment
 - **Isotope Tracking:** Natively supports tracking labeled isotopes and generating corresponding parallel reactions.
 
 ## Installation
+You can install PyAntiGen into your Python environment with:
+```bash
+pip install pyantigen
+```
 
-You can install PyAntiGen globally into your preferred Python environment by cloning this repository and running pip:
+You can also install PyAntiGen globally into your preferred Python environment by cloning this repository and running pip:
 
 ```bash
 git clone https://github.com/elbert5770/PyAntiGen.git
@@ -49,7 +53,7 @@ pip install -e .
 
 Because PyAntiGen is installed as a system-level Python package, you don't need a copy of the framework files in your working directory. 
 
-To start a brand new modeling workspace, just open a terminal and navigate to a folder where you want it to live (not PyAntiGen) and run:
+To start a brand new modeling workspace, just open a terminal and navigate to a folder where you want your project to live (be careful not to build within the PyAntiGen folder itself) and run:
 
 ```bash
 pyantigen-create MyNewModel
@@ -60,18 +64,16 @@ This will automatically scaffold the following project directory:
 MyNewModel/
 ├── .agents/
 │   └── skills/          (agent skills, e.g. module generation, ODE conversion)
-├── scripts/
-│   ├── Example/         (full example: generate, run, optimize + Modules/)
-│   │   ├── Example_generate.py
-│   │   ├── Example_run.py
-│   │   ├── Example_optimize.py
+├── Projects/
+│   ├── Example/         (full example: generate, run + Modules/, Engine/)
+│   │   ├── Model_generate.py
+│   │   ├── Model_run.py
 │   │   └── Modules/     (Data, AntimonyGen, Plots, Simulate, Optimize, Experiment, Events)
-│   └── MyNewModel/      (same structure, Modules/ left empty for your code)
-│       ├── MyNewModel_generate.py
-│       ├── MyNewModel_run.py
-│       ├── MyNewModel_optimize.py
+│   └── MyNewModel/      (same structure, Modules/ pre-populated from Example)
+│       ├── Model_generate.py
+│       ├── Model_run.py
 │       └── Modules/     (Data, AntimonyGen, Plots, Simulate, Optimize, Experiment, Events)
-├── modules/
+├── antimony_modules/
 │   └── __init__.py      (plus Basic/ for the example)
 ├── data/                (Example experiment CSVs copied for the example)
 ├── antimony_models/
@@ -79,36 +81,41 @@ MyNewModel/
 ├── generated/
 │   └── Example/         (reaction dict, rules, etc. after generate)
 ├── results/
-│   └── Example/         (plots from Example_run.py)
+│   └── Example/         (plots from Model_run.py)
 ├── SBML_models/
 └── pyantigen_settings.json   (e.g. archive_with_timestamp: false)
 ```
 
-All model-specific files are grouped under folders named by `MODEL_NAME` (e.g. `Example` or your project name). From `MyNewModel/scripts/Example/` run:
+Every project folder under `Projects/` has a script called `Model_generate.py` that is run to generate the model. `MODEL_NAME` is derived automatically from the enclosing folder name (see `AntiGen_paths.py`), so being in the right project folder is all that's needed to generate/run the correct project. From `MyNewModel/Projects/Example/` run:
 
 ```bash
-python Example_generate.py
+python Model_generate.py
 ```
 
-This generates the model and writes outputs to `antimony_models/Example/` and `generated/Example/`. Edit parameters if desired in `antimony_models/Example/Example_parameters.csv`, then run:
+This generates the model from the specified files in 'antimony_modules' and writes outputs to `antimony_models/Example/` and `generated/Example/`. This is entirely optional as Model_run.py also calls the constructor functions in `Model_generate.py`.
+
+To run a simulation or optimization, you may edit the parameters in `antimony_models/Example/Example_parameters.csv`, derived parameters in `antimony_models/Example/Example_manual.txt`, and initial conditions in `antimony_models/Example/Example_InitialConditions.csv`.
+
+Then, run `Model_run.py` to simulate the Example in Tellurium/RoadRunner:
 
 ```bash
-python Example_run.py
+python Model_run.py --simulate Example
 ```
 
-For parameter fitting against data, run:
+To run optimization examples use the --optimize flag:
 
 ```bash
-python Example_optimize.py
+python Model_run.py --optimize Example1
+python Model_run.py --optimize Example2
+python Model_run.py --optimize Example3
 ```
 
-Your own model lives under `scripts/MyNewModel/` with the same files as the Example. Modify the code for your model in `scripts/MyNewModel/Modules/` and `scripts/MyNewModel/MyNewModel_generate.py`, `scripts/MyNewModel/MyNewModel_run.py`, and `scripts/MyNewModel/MyNewModel_optimize.py'. Your problem will also require new modules in folder 'modules'.
+Your own model lives under `Projects/MyNewModel/`. Modify the code for your model in `Projects/MyNewModel/Modules/`, `Projects/MyNewModel/Model_generate.py`, and `Projects/MyNewModel/Model_run.py`. Your problem will also require new modules in `antimony_modules/` to define the model.
 
-Keeping the generation and simulation steps separate gives you time to adjust parameters and inspect the generated files before running.
 
 ### Running from an IDE (Cursor / VS Code)
 
 The **Play** button uses whichever Python interpreter is currently selected. If your environment (conda/venv) isn’t loaded, the run may fail with import or path errors.
 
 1. **Select the correct interpreter**: `Ctrl+Shift+P` (or `Cmd+Shift+P` on macOS) → **Python: Select Interpreter** → choose the environment where you ran `pip install -e .` (e.g. your conda or venv).
-2. **Run from project root**: Open the *project* folder (e.g. `MyNewModel`) as the workspace. Use **Run and Debug** (or Play on `scripts/Example/Example_run.py`); the project root is resolved from the script location so `antimony_models/Example/`, `generated/Example/`, and `results/Example/` resolve correctly.
+2. **Run from project root**: Open the *project* folder (e.g. `MyNewModel`) as the workspace. Use **Run and Debug** (or Play on `Projects/Example/Model_run.py`); the project root is resolved from the script location so `antimony_models/Example/`, `generated/Example/`, and `results/Example/` resolve correctly.

{pyantigen-1.0.4 → pyantigen-1.0.7}/PyAntiGen.egg-info/SOURCES.txt

@@ -6,6 +6,7 @@ setup.py
 PyAntiGen.egg-info/PKG-INFO
 PyAntiGen.egg-info/SOURCES.txt
 PyAntiGen.egg-info/dependency_links.txt
+PyAntiGen.egg-info/entry_points.txt
 PyAntiGen.egg-info/requires.txt
 PyAntiGen.egg-info/top_level.txt
 framework/AntimonyGen.py
@@ -23,8 +24,18 @@ framework/pyantigen.py
 framework/rate_laws.py
 framework/reaction_creation.py
 framework/template/Example/AntiGen_paths.py
-framework/template/Example/Example_generate.py
-framework/template/Example/Example_run.py
+framework/template/Example/Model_generate.py
+framework/template/Example/Model_run.py
+framework/template/Example/Engine/Evaluator.py
+framework/template/Example/Engine/Model_optimize.py
+framework/template/Example/Engine/Model_simulate.py
+framework/template/Example/Engine/Nuisance_sensitivity.py
+framework/template/Example/Engine/Optimize.py
+framework/template/Example/Engine/Petab_export.py
+framework/template/Example/Engine/Profile_checkpoint.py
+framework/template/Example/Engine/Results.py
+framework/template/Example/Engine/Sensitivity_analysis.py
+framework/template/Example/Engine/Simulate.py
 framework/template/Example/Modules/Data.py
 framework/template/Example/Modules/Events.py
 framework/template/Example/Modules/Experiment.py
@@ -33,6 +44,7 @@ framework/template/Example/Modules/Observed_species.py
 framework/template/Example/Modules/Optimizer_settings.py
 framework/template/Example/Modules/Plots.py
 framework/template/Example/Modules/Solver_settings.py
+framework/template/Example/Modules/Update_opt_parameters.py
 framework/template/Example/Modules/Update_parameters.py
 framework/template/data/ADneg.csv
 framework/template/data/ADpos.csv

pyantigen-1.0.7/PyAntiGen.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pyantigen-create = framework.cli:create_project

{pyantigen-1.0.4 → pyantigen-1.0.7}/README.md

@@ -10,8 +10,12 @@ PyAntiGen is a declarative, object-oriented framework for generating compartment
 - **Isotope Tracking:** Natively supports tracking labeled isotopes and generating corresponding parallel reactions.
 
 ## Installation
+You can install PyAntiGen into your Python environment with:
+```bash
+pip install pyantigen
+```
 
-You can install PyAntiGen globally into your preferred Python environment by cloning this repository and running pip:
+You can also install PyAntiGen globally into your preferred Python environment by cloning this repository and running pip:
 
 ```bash
 git clone https://github.com/elbert5770/PyAntiGen.git
@@ -23,7 +27,7 @@ pip install -e .
 
 Because PyAntiGen is installed as a system-level Python package, you don't need a copy of the framework files in your working directory. 
 
-To start a brand new modeling workspace, just open a terminal and navigate to a folder where you want it to live (not PyAntiGen) and run:
+To start a brand new modeling workspace, just open a terminal and navigate to a folder where you want your project to live (be careful not to build within the PyAntiGen folder itself) and run:
 
 ```bash
 pyantigen-create MyNewModel
@@ -34,18 +38,16 @@ This will automatically scaffold the following project directory:
 MyNewModel/
 ├── .agents/
 │   └── skills/          (agent skills, e.g. module generation, ODE conversion)
-├── scripts/
-│   ├── Example/         (full example: generate, run, optimize + Modules/)
-│   │   ├── Example_generate.py
-│   │   ├── Example_run.py
-│   │   ├── Example_optimize.py
+├── Projects/
+│   ├── Example/         (full example: generate, run + Modules/, Engine/)
+│   │   ├── Model_generate.py
+│   │   ├── Model_run.py
 │   │   └── Modules/     (Data, AntimonyGen, Plots, Simulate, Optimize, Experiment, Events)
-│   └── MyNewModel/      (same structure, Modules/ left empty for your code)
-│       ├── MyNewModel_generate.py
-│       ├── MyNewModel_run.py
-│       ├── MyNewModel_optimize.py
+│   └── MyNewModel/      (same structure, Modules/ pre-populated from Example)
+│       ├── Model_generate.py
+│       ├── Model_run.py
 │       └── Modules/     (Data, AntimonyGen, Plots, Simulate, Optimize, Experiment, Events)
-├── modules/
+├── antimony_modules/
 │   └── __init__.py      (plus Basic/ for the example)
 ├── data/                (Example experiment CSVs copied for the example)
 ├── antimony_models/
@@ -53,36 +55,41 @@ MyNewModel/
 ├── generated/
 │   └── Example/         (reaction dict, rules, etc. after generate)
 ├── results/
-│   └── Example/         (plots from Example_run.py)
+│   └── Example/         (plots from Model_run.py)
 ├── SBML_models/
 └── pyantigen_settings.json   (e.g. archive_with_timestamp: false)
 ```
 
-All model-specific files are grouped under folders named by `MODEL_NAME` (e.g. `Example` or your project name). From `MyNewModel/scripts/Example/` run:
+Every project folder under `Projects/` has a script called `Model_generate.py` that is run to generate the model. `MODEL_NAME` is derived automatically from the enclosing folder name (see `AntiGen_paths.py`), so being in the right project folder is all that's needed to generate/run the correct project. From `MyNewModel/Projects/Example/` run:
 
 ```bash
-python Example_generate.py
+python Model_generate.py
 ```
 
-This generates the model and writes outputs to `antimony_models/Example/` and `generated/Example/`. Edit parameters if desired in `antimony_models/Example/Example_parameters.csv`, then run:
+This generates the model from the specified files in 'antimony_modules' and writes outputs to `antimony_models/Example/` and `generated/Example/`. This is entirely optional as Model_run.py also calls the constructor functions in `Model_generate.py`.
+
+To run a simulation or optimization, you may edit the parameters in `antimony_models/Example/Example_parameters.csv`, derived parameters in `antimony_models/Example/Example_manual.txt`, and initial conditions in `antimony_models/Example/Example_InitialConditions.csv`.
+
+Then, run `Model_run.py` to simulate the Example in Tellurium/RoadRunner:
 
 ```bash
-python Example_run.py
+python Model_run.py --simulate Example
 ```
 
-For parameter fitting against data, run:
+To run optimization examples use the --optimize flag:
 
 ```bash
-python Example_optimize.py
+python Model_run.py --optimize Example1
+python Model_run.py --optimize Example2
+python Model_run.py --optimize Example3
 ```
 
-Your own model lives under `scripts/MyNewModel/` with the same files as the Example. Modify the code for your model in `scripts/MyNewModel/Modules/` and `scripts/MyNewModel/MyNewModel_generate.py`, `scripts/MyNewModel/MyNewModel_run.py`, and `scripts/MyNewModel/MyNewModel_optimize.py'. Your problem will also require new modules in folder 'modules'.
+Your own model lives under `Projects/MyNewModel/`. Modify the code for your model in `Projects/MyNewModel/Modules/`, `Projects/MyNewModel/Model_generate.py`, and `Projects/MyNewModel/Model_run.py`. Your problem will also require new modules in `antimony_modules/` to define the model.
 
-Keeping the generation and simulation steps separate gives you time to adjust parameters and inspect the generated files before running.
 
 ### Running from an IDE (Cursor / VS Code)
 
 The **Play** button uses whichever Python interpreter is currently selected. If your environment (conda/venv) isn’t loaded, the run may fail with import or path errors.
 
 1. **Select the correct interpreter**: `Ctrl+Shift+P` (or `Cmd+Shift+P` on macOS) → **Python: Select Interpreter** → choose the environment where you ran `pip install -e .` (e.g. your conda or venv).
-2. **Run from project root**: Open the *project* folder (e.g. `MyNewModel`) as the workspace. Use **Run and Debug** (or Play on `scripts/Example/Example_run.py`); the project root is resolved from the script location so `antimony_models/Example/`, `generated/Example/`, and `results/Example/` resolve correctly.
+2. **Run from project root**: Open the *project* folder (e.g. `MyNewModel`) as the workspace. Use **Run and Debug** (or Play on `Projects/Example/Model_run.py`); the project root is resolved from the script location so `antimony_models/Example/`, `generated/Example/`, and `results/Example/` resolve correctly.

{pyantigen-1.0.4 → pyantigen-1.0.7}/framework/AntimonyGen.py

@@ -24,7 +24,7 @@ def AntimonyGen(MODEL_NAME, repo_root=None):
  
     if not model_text.strip():
         raise RuntimeError(
-            f"No model content loaded. Generate the model first: python {MODEL_NAME}_generate.py"
+            "No model content loaded. Generate the model first: python Model_generate.py"
         )
 
     events_path = os.path.join(repo_root, "generated", MODEL_NAME, MODEL_NAME + "_events.txt")

pyantigen-1.0.7/framework/TelluriumGen.py

@@ -0,0 +1,16 @@
+import tellurium as te
+from framework.antimony_utils import archive_antimony_snapshot
+
+def TelluriumGen(model_text, paths, settings=None ):
+    print("Loading model into Tellurium...")
+    try:
+        r = te.loada(model_text)
+    except Exception as e:
+        raise RuntimeError(f"Error loading model: {e}") from e
+
+    if settings is not None:
+        if settings["save_SBML?"]:
+            sbml_content = r.getSBML()
+            archive_dir = archive_antimony_snapshot(paths["MODEL_NAME"], paths["repo_root"], sbml_content=sbml_content)
+            print(f"Archive and SBML written to: {archive_dir}")
+    return r

{pyantigen-1.0.4 → pyantigen-1.0.7}/framework/cli.py

@@ -181,15 +181,14 @@ def create_project():
     os.makedirs(project_generated_dir, exist_ok=True)
     os.makedirs(project_results_dir, exist_ok=True)
 
-    # Copy Example Projects into project folder (MODEL_NAME derived from folder name at runtime)
+    # Copy Model_generate.py / Model_run.py into project folder (MODEL_NAME derived from folder name at runtime)
     if os.path.isdir(example_template):
-        for base in ("Example_generate", "Example_run"):
+        for base in ("Model_generate", "Model_run"):
             src = os.path.join(example_template, base + ".py")
             if os.path.isfile(src):
-                dst_name = project_dir + base[7:]  # "Example_foo" -> "{project_dir}_foo"
-                dst = os.path.join(project_Projects_dir, dst_name + ".py")
+                dst = os.path.join(project_Projects_dir, base + ".py")
                 shutil.copy2(src, dst)
-                print(f"  Created file: Projects/{project_dir}/{dst_name}.py")
+                print(f"  Created file: Projects/{project_dir}/{base}.py")
         
         # Also copy AntiGen_paths.py utility
         paths_src = os.path.join(example_template, "AntiGen_paths.py")