pull from master

.gitattributes

@@ -0,0 +1,2 @@
+*.py linguist-language=python
+*.ipynb linguist-documentation

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     timeout-minutes: 20
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -33,13 +33,11 @@ jobs:
     - name: Install dependencies
       run: |
         pip install pytest-cov
-        pip install numpy
-        pip install Cython
         pip install codecov
-        make install
+        pip install .
     - name: Test with pytest
       run: |
-        python -m pytest -vv test/ --cov-report=xml --cov=cassiopeia
+        pytest -vv test/ --cov-report=xml --cov=cassiopeia
     - name: After success
       run: |
         codecov

.gitignore

@@ -1,3 +1,156 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
 .DS_Store
 .idea
 *.pyc
@@ -10,3 +163,5 @@ build
 *.c
 stdout.log
 notebooks/.ipynb_checkpoints
+cassiopeia/tools/branch_length_estimator/_iid_exponential_bayesian.cpp
+docs/api/reference/**

.readthedocs.yml

@@ -4,10 +4,9 @@ build:
 sphinx:
   configuration: docs/conf.py
 python:
-  version: 3.6
+  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
-      - docs
-    - requirements: docs/requirements.txt
+      - docs

MANIFEST.in

@@ -1,3 +1,2 @@
-include cassiopeia/preprocess/*.pyx
-include cassiopeia/solver/*.pyx
-include *.toml
+include LICENSE
+recursive-include cassiopeia *

Makefile

@@ -17,24 +17,12 @@ clean_sdist:
 
 clean: clean_develop clean_pypi
 
-install: 
-	- $(python) setup.py build
-	- $(python) setup.py build_ext --inplace
-	- $(python) -m pip install --user .
+install:
+	- $(python) -m pip install .
 
 check_build_reqs:
 	@$(python) -c 'import pytest' \
                 || ( printf "$(redpip)Build requirements are missing. Run 'make prepare' to install them.$(normal)" ; false )
 
 test: check_build_reqs
-	$(python) -m pytest -vv $(tests)
-
-
-pypi: clean clean_sdist
-	set -x \
-	&& $(python) setup.py sdist bdist_wheel \
-	&& twine check dist/* \
-	&& twine upload --repository-url https://test.pypi.org/legacy/ dist/*
-
-clean_pypi:
-	- rm -rf build/
+	$(python) -m pytest -vv $(tests)

README.md

@@ -29,22 +29,31 @@ Free Software: MIT License
 Installation
 --------------
 
+For users:
+
+```
+pip install git+https://github.com/YosefLab/Cassiopeia@master#egg=cassiopeia-lineage
+```
+
+For developers:
+
 1. Clone the package as so: ``git clone https://github.com/YosefLab/Cassiopeia.git``
 
-2. Ensure that you have python3.6 installed. You can install this via pip.
+2. Ensure that you have Python >= 3.7 installed. (Python 3.6 may still work, but is not guaranteed.) We prefer using [miniconda](https://docs.conda.io/en/latest/miniconda.html).
 
-3. Make sure that Gurobi is installed. You can follow the instructions listed [here](http://www.gurobi.com/academia/for-universities). To verify that it's working correctly, use the following tests:
+3. [Optional] Make sure that Gurobi is installed. You can follow the instructions listed [here](http://www.gurobi.com/academia/for-universities). To verify that it's working correctly, use the following tests:
     * Run the command ``gurobi.sh`` from a terminal window
     * From the Gurobi installation directory (where there is a setup.py file), use ``python setup.py install --user``
-    
-4. Install Cassiopeia by first making sure you have stable version of `Cython` and `pytest`. Then, you can install Cassiopeia by running `make install` from the directory where you have Cassiopeia downloaded.
-    
-To verify that it installed correctly, try running our tests with `make test`.
+
+4. Install Cassiopeia by first changing into the Cassiopeia directory and then `pip3 install .`. To install dev and docs requirements, you can run `pip3 install .[dev,docs]`.
+
+To verify that it installed correctly, try running our tests with `pytest`.
 
 Reference
 ----------------------
 
 If you've found Cassiopeia useful for your research, please consider citing our paper published in Genome Biology:
 
-
+```
 Matthew G Jones*, Alex Khodaverdian*, Jeffrey J Quinn*, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonathan S Weissman, Nir Yosef. (2020), [*Inference of single-cell phylogenies from lineage tracing data using Cassiopeia*](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02000-8), Genome Biology
+```

build.py

@@ -0,0 +1,61 @@
+import os
+import shutil
+from distutils.command.build_ext import build_ext
+from distutils.core import Distribution, Extension
+
+import numpy
+from Cython.Build import cythonize
+
+# https://github.com/mdgoldberg/poetry-cython-example
+
+
+def build():
+    extensions = [
+        Extension(
+            "cassiopeia.preprocess.collapse_cython",
+            ["cassiopeia/preprocess/collapse_cython.pyx"],
+        ),
+        Extension(
+            "cassiopeia.solver.ilp_solver_utilities",
+            ["cassiopeia/solver/ilp_solver_utilities.pyx"],
+            include_dirs=[numpy.get_include()],
+        ),
+        Extension(
+            "cassiopeia.tools.branch_length_estimator._iid_exponential_bayesian",
+            sources=[
+                "cassiopeia/tools/branch_length_estimator/_iid_exponential_bayesian.pyx",
+                "cassiopeia/tools/branch_length_estimator/_iid_exponential_bayesian_cpp.cpp",
+            ],
+            extra_compile_args=[
+                "-std=c++17",
+                "-Wall",
+                "-Wextra",
+                "-pedantic",
+                "-O3",
+            ],
+            language="c++",
+        ),
+    ]
+    ext_modules = cythonize(
+        extensions,
+        compiler_directives={"language_level": 3},
+    )
+
+    distribution = Distribution({"name": "extended", "ext_modules": ext_modules})
+    distribution.package_dir = "extended"
+
+    cmd = build_ext(distribution)
+    cmd.ensure_finalized()
+    cmd.run()
+
+    # Copy built extensions back to the project
+    for output in cmd.get_outputs():
+        relative_extension = os.path.relpath(output, cmd.build_lib)
+        shutil.copyfile(output, relative_extension)
+        mode = os.stat(relative_extension).st_mode
+        mode |= (mode & 0o444) >> 2
+        os.chmod(relative_extension, mode)
+
+
+if __name__ == "__main__":
+    build()

cassiopeia/__init__.py

@@ -2,15 +2,26 @@
 
 """Top-level for Cassiopeia development."""
 
-package_name = "cassiopeia"
-__author__ = "Matt Jones, Alex Khodaveridan, Richard Zhang, Sebastian Prillo"
-__email__ = "mattjones315@berkeley.edu"
-__version__ = "0.0.1"
-
-from . import pp
+from . import preprocess as pp
 from . import solver
-from . import pl
+from . import plotting as pl
 from . import data
 from . import critique
-from . import sim
-from . import tl
+from . import simulator as sim
+from . import tools as tl
+
+# https://github.com/python-poetry/poetry/pull/2366#issuecomment-652418094
+# https://github.com/python-poetry/poetry/issues/144#issuecomment-623927302
+try:
+    import importlib.metadata as importlib_metadata
+except ModuleNotFoundError:
+    import importlib_metadata
+package_name = "cassiopeia-lineage"
+__version__ = importlib_metadata.version(package_name)
+
+import sys
+
+sys.modules.update({f"{__name__}.{m}": globals()[m] for m in ["tl", "pp", "pl", "sim"]})
+del sys
+
+__all__ = ["pp", "solver", "pl", "data", "critique", "sim", "tl"]

cassiopeia/critique/__init__.py

@@ -1,7 +1,3 @@
 """Top level for the cassiopeia critique module."""
 
-__author__ = "Matt Jones, Richard Zhang"
-__email__ = "mattjones315@berkeley.edu"
-__version__ = "0.0.1"
-
 from .compare import robinson_foulds, triplets_correct

cassiopeia/mixins/errors.py

@@ -110,5 +110,9 @@ class TreeMetricError(Exception):
 
 class ParameterEstimateError(Exception):
     """An Exception class for the estimation and retrieval of tree parameters"""
+
+    pass
 
+
+class PlottingError(Exception):
     pass