msasim 2024.5.22__tar.gz → 2024.5.221247__tar.gz

msasim-2024.5.221247/PKG-INFO

@@ -0,0 +1,54 @@
+Metadata-Version: 2.1
+Name: msasim
+Version: 2024.5.221247
+Summary: A fast MSA simulator
+Home-page: https://github.com/elyawy/Sailfish-backend
+Author: Elya Wygoda
+Author-email: elya.wygoda@gmail.com
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+
+# Sailfish
+
+Sailfish is a performant multiple sequence alignment(MSA) simulator, written in C++ and Python, allowing for quick and easy generation of large simulated datasets. 
+
+## Project goals
+
+- Ease of use
+- Speed
+- Modularity
+
+## Installation
+
+```bash
+pip install msasim
+```
+
+## Example
+
+```python
+from msasim import sailfish as sim
+from msasim.sailfish import MODEL_CODES, ZipfDistribution
+
+ROOT_SEQUENCE_LENGTH = 100
+
+sim_protocol = sim.SimProtocol("(A:0.5,B:0.5);",
+                               deletion_rate=0.01,
+                               insertion_rate=0.01,
+                               deletion_dist=ZipfDistribution(1.08, 50),
+                               insertion_dist=ZipfDistribution(1.08, 50),
+                               seed=50)
+sim_protocol.set_sequence_size(ROOT_SEQUENCE_LENGTH)
+
+simulation = sim.Simulator(sim_protocol, simulation_type=sim.SIMULATION_TYPE.PROTEIN)
+
+simulation.set_replacement_model(model=MODEL_CODES.WAG, 
+                                 gamma_parameters_alpha=1.0, 
+                                 gamma_parameters_catergories=4)
+msa = simulation()
+msa.print_msa()
+
+```

msasim-2024.5.221247/README.md

@@ -0,0 +1,41 @@
+# Sailfish
+
+Sailfish is a performant multiple sequence alignment(MSA) simulator, written in C++ and Python, allowing for quick and easy generation of large simulated datasets. 
+
+## Project goals
+
+- Ease of use
+- Speed
+- Modularity
+
+## Installation
+
+```bash
+pip install msasim
+```
+
+## Example
+
+```python
+from msasim import sailfish as sim
+from msasim.sailfish import MODEL_CODES, ZipfDistribution
+
+ROOT_SEQUENCE_LENGTH = 100
+
+sim_protocol = sim.SimProtocol("(A:0.5,B:0.5);",
+                               deletion_rate=0.01,
+                               insertion_rate=0.01,
+                               deletion_dist=ZipfDistribution(1.08, 50),
+                               insertion_dist=ZipfDistribution(1.08, 50),
+                               seed=50)
+sim_protocol.set_sequence_size(ROOT_SEQUENCE_LENGTH)
+
+simulation = sim.Simulator(sim_protocol, simulation_type=sim.SIMULATION_TYPE.PROTEIN)
+
+simulation.set_replacement_model(model=MODEL_CODES.WAG, 
+                                 gamma_parameters_alpha=1.0, 
+                                 gamma_parameters_catergories=4)
+msa = simulation()
+msa.print_msa()
+
+```

msasim-2024.5.221247/msasim.egg-info/PKG-INFO

@@ -0,0 +1,54 @@
+Metadata-Version: 2.1
+Name: msasim
+Version: 2024.5.221247
+Summary: A fast MSA simulator
+Home-page: https://github.com/elyawy/Sailfish-backend
+Author: Elya Wygoda
+Author-email: elya.wygoda@gmail.com
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+
+# Sailfish
+
+Sailfish is a performant multiple sequence alignment(MSA) simulator, written in C++ and Python, allowing for quick and easy generation of large simulated datasets. 
+
+## Project goals
+
+- Ease of use
+- Speed
+- Modularity
+
+## Installation
+
+```bash
+pip install msasim
+```
+
+## Example
+
+```python
+from msasim import sailfish as sim
+from msasim.sailfish import MODEL_CODES, ZipfDistribution
+
+ROOT_SEQUENCE_LENGTH = 100
+
+sim_protocol = sim.SimProtocol("(A:0.5,B:0.5);",
+                               deletion_rate=0.01,
+                               insertion_rate=0.01,
+                               deletion_dist=ZipfDistribution(1.08, 50),
+                               insertion_dist=ZipfDistribution(1.08, 50),
+                               seed=50)
+sim_protocol.set_sequence_size(ROOT_SEQUENCE_LENGTH)
+
+simulation = sim.Simulator(sim_protocol, simulation_type=sim.SIMULATION_TYPE.PROTEIN)
+
+simulation.set_replacement_model(model=MODEL_CODES.WAG, 
+                                 gamma_parameters_alpha=1.0, 
+                                 gamma_parameters_catergories=4)
+msa = simulation()
+msa.print_msa()
+
+```

{msasim-2024.5.22 → msasim-2024.5.221247}/msasim.egg-info/SOURCES.txt

@@ -2,8 +2,8 @@ LICENSE
 README.md
 pyproject.toml
 setup.py
-Sailfish/__init__.py
-Sailfish/simulator.py
+msasim/__init__.py
+msasim/sailfish.py
 msasim.egg-info/PKG-INFO
 msasim.egg-info/SOURCES.txt
 msasim.egg-info/dependency_links.txt

{msasim-2024.5.22 → msasim-2024.5.221247}/msasim.egg-info/top_level.txt

@@ -1,2 +1,2 @@
-Sailfish
 _Sailfish
+msasim

{msasim-2024.5.22 → msasim-2024.5.221247}/setup.py

@@ -6,9 +6,9 @@ from setuptools import setup, find_packages
 
 from datetime import datetime
 
-today = datetime.today()
+now = datetime.now()
 
-__version__ = f"{today.year}.{today.month}.{today.day}"
+__version__ = f"{now.year}.{now.month}.{now.day}{now.hour}{now.minute}"
 
 # The main interface is through Pybind11Extension.
 # * You can add cxx_std=11/14/17, and then build_ext can be removed.
@@ -44,11 +44,13 @@ setup(
     author_email="elya.wygoda@gmail.com",
     url="https://github.com/elyawy/Sailfish-backend",
     description="A fast MSA simulator",
-    long_description="Sailfish is a performant multiple sequence alignment simulator, written in C++, allowing fast generation of large simualted datasets.",
+    # long_description="Sailfish is a performant multiple sequence alignment simulator, written in C++, allowing fast generation of large simualted datasets.",
+    long_description=open("README.md", 'r').read(),
+    long_description_content_type='text/markdown',
     ext_modules=ext_modules,
     extras_require={"test": "pytest"},
     cmdclass={"build_ext": build_ext},
     zip_safe=False,
     python_requires=">=3.6",
-    packages=find_packages(include=['Sailfish','tests'])
+    packages=find_packages(include=['msasim','tests'])
 )

msasim-2024.5.22/PKG-INFO

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: msasim
-Version: 2024.5.22
-Summary: A fast MSA simulator
-Home-page: https://github.com/elyawy/Sailfish-backend
-Author: Elya Wygoda
-Author-email: elya.wygoda@gmail.com
-Requires-Python: >=3.6
-License-File: LICENSE
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-
-Sailfish is a performant multiple sequence alignment simulator, written in C++, allowing fast generation of large simualted datasets.

msasim-2024.5.22/README.md

@@ -1,2 +0,0 @@
-# Sailfish-backend
-Backend C++ code for the Sailfish MSA simulation library using the Pybind11 framework

msasim-2024.5.22/msasim.egg-info/PKG-INFO

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: msasim
-Version: 2024.5.22
-Summary: A fast MSA simulator
-Home-page: https://github.com/elyawy/Sailfish-backend
-Author: Elya Wygoda
-Author-email: elya.wygoda@gmail.com
-Requires-Python: >=3.6
-License-File: LICENSE
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-
-Sailfish is a performant multiple sequence alignment simulator, written in C++, allowing fast generation of large simualted datasets.