Merge pull request #12 from faridrashidi/release/v0.0.9

release v0.0.9

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.8
+current_version = 0.0.9
 commit = True
 tag = False
 files = setup.py trisicell/__init__.py

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
     -   id: mixed-line-ending
         args: [--fix=lf]
     -   id: trailing-whitespace
-        exclude: ^.bumpversion.cfg$  # trailing whitespace
+        exclude: ^.bumpversion.cfg$
     -   id: check-case-conflict
     -   id: check-docstring-first
     # -   id: check-yaml
@@ -45,10 +45,10 @@ repos:
     -   id: script-must-have-extension
         name: Check executable files use .sh extension
         types: [shell, executable]
-# -   repo: https://github.com/myint/rstcheck
-#     rev: 3f92957478422df87bd730abde66f089cc1ee19b
-#     hooks:
-#     -   id: rstcheck
+-   repo: https://github.com/myint/rstcheck
+    rev: 3f92957478422df87bd730abde66f089cc1ee19b
+    hooks:
+    -   id: rstcheck
 -   repo: https://github.com/asottile/blacken-docs
     rev: v1.10.0
     hooks:
@@ -67,7 +67,24 @@ repos:
     -   id: rst-backticks
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
-# -   repo: https://github.com/PyCQA/doc8
-#     rev: 0.9.0a1
+-   repo: https://github.com/PyCQA/doc8
+    rev: 0.9.0a1
+    hooks:
+    -   id: doc8
+        args: [--max-line-length=88]
+# -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+#     rev: v2.0.0
 #     hooks:
-#     -   id: doc8
+#     -   id: pretty-format-yaml
+#         args: [--autofix, --indent, '4']
+-   repo: https://github.com/PyCQA/flake8
+    rev: 3.9.0
+    hooks:
+    -   id: flake8
+        additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-comprehensions, flake8-bugbear, flake8-blind-except]
+        args: [--max-line-length=88, --config=setup.cfg]
+-   repo: https://github.com/asottile/yesqa
+    rev: v1.2.2
+    hooks:
+    -   id: yesqa
+        additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-comprehensions, flake8-bugbear, flake8-blind-except]

.rstcheck.cfg

@@ -1,3 +1,3 @@
 [rstcheck]
-ignore_messages=(Unknown target name:.*|No (directive|role) entry for "(auto)?(class|method|property|function|func|mod|module)" in module "docutils\.parsers\.rst\.languages\.en"\.)
+ignore_messages=( No directive entry for.*|Hyperlink target.*|Unknown target name:.*|No (directive|role) entry for "(auto)?(class|method|property|function|func|mod|module)" in module "docutils\.parsers\.rst\.languages\.en"\.)
 report=info

CONTRIBUTING.rst

@@ -1,7 +1,11 @@
 Contributing guidelines
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Welcome to `Trisicell <https://github.com/faridrashidi/trisicell>`_! Before sending your pull requests, make sure that you **read the whole guidelines**. If you have any doubt on the contributing guide, please feel free to `state it clearly in an issue <https://github.com/faridrashidi/trisicell/issues/new/choose>`_.
+Welcome to `Trisicell project <https://github.com/faridrashidi/trisicell>`_!
+Before sending your pull requests, make sure that you **read the whole
+guidelines**. If you have any doubt on the contributing guide, please
+feel free to `state it clearly in an
+issue <https://github.com/faridrashidi/trisicell/issues/new/choose>`_.
 
 Table of Contents
 =================
@@ -26,7 +30,8 @@ Install the development mode::
 
     pip install -e '.[dev]'
 
-Then install pre-commit. This will ensure that the pushed code passes the linting steps::
+Then install pre-commit. This will ensure that the pushed code passes the
+linting steps::
 
     pre-commit install
 
@@ -37,13 +42,21 @@ The Trisicell project:
 
 - `trisicell <trisicell>`_: the root of the package.
 
-    - `trisicell/io <trisicell/io>`_: the read/write module, offers a bunch of functions for reading and writing of the data.
-    - `trisicell/pl <trisicell/pl>`_: the plotting module, offers plotting the tree in clonal or dendrogram format.
-    - `trisicell/pp <trisicell/pp>`_: the preprocessing module, offers a bunch of functions for filtering and preprocessing of the data.
-    - `trisicell/tl <trisicell/tl>`_: the tools module, offers a high-level API to compute the conflict-free solution and calculating the probability of mutations seeding particular cells.
-    - `trisicell/ul <trisicell/ul>`_: the utils module, offers a bunch of utility functions.
-    - `trisicell/commands <trisicell/commands>`_: the CLI commands module, offers running trisicell in command-line interface (CLI) mode
-    - `trisicell/datasets <trisicell/datasets>`_: the datasets module, offers some of the published single-cell datasets and generating simulations
+    - `trisicell/io <trisicell/io>`_: the read/write module, offers a bunch of
+        functions for reading and writing of the data.
+    - `trisicell/pl <trisicell/pl>`_: the plotting module, offers plotting the
+        tree in clonal or dendrogram format.
+    - `trisicell/pp <trisicell/pp>`_: the preprocessing module, offers a bunch
+        of functions for filtering and preprocessing of the data.
+    - `trisicell/tl <trisicell/tl>`_: the tools module, offers a high-level API
+        to compute the conflict-free solution and calculating the probability of
+        mutations seeding particular cells.
+    - `trisicell/ul <trisicell/ul>`_: the utils module, offers a bunch of
+        utility functions.
+    - `trisicell/commands <trisicell/commands>`_: the CLI commands module,
+        offers running trisicell in command-line interface (CLI) mode.
+    - `trisicell/datasets <trisicell/datasets>`_: the datasets module, offers
+        some of the published single-cell datasets and generating simulations.
 
 Tests structure:
 
@@ -52,12 +65,14 @@ Tests structure:
 
 Code style guide
 ----------------
-We rely on ``black`` and ``isort`` to do the most of the formatting - both of them are integrated as pre-commit hooks.
-You can use ``pre-commit`` to check the changes::
+We rely on ``black`` and ``isort`` to do the most of the formatting - both of
+them are integrated as pre-commit hooks. You can use ``pre-commit`` to check
+the changes::
 
     make lint
 
-Keep in mind to use tags like ``TODO[colon]`` and ``FIXME[colon]`` to make other developers aware of what to do next.
+Keep in mind to use tags like ``TODO[colon]`` and ``FIXME[colon]`` to make
+other developers aware of what to do next.
 
 
 Testing
@@ -69,10 +84,13 @@ We use ``pytest`` to automate our testing. To execute the tests, run::
 
 Writing documentation
 ---------------------
-We use ``numpy``-style docstrings for the documentation with the following additions and modifications:
+We use ``numpy``-style docstrings for the documentation with the following
+additions and modifications:
 
-- when referring to some argument within the same docstring, enclose that reference in \`\`.
-- prefer putting references in the ``references.bib`` instead under the ``References`` sections of the docstring.
+- when referring to some argument within the same docstring, enclose that
+    reference in \`\`.
+- prefer putting references in the ``references.bib`` instead under the
+    ``References`` sections of the docstring.
 
 In order to build the documentation, run::
 
@@ -83,29 +101,42 @@ Building c files
 ----------------
 For building ``.cpp`` files from ``.pyx`` files you need to execute::
 
-    CYTHONIZE=1 pip install -e .
+    CYTHONIZE=1 python setup.py install
+    pip install -e .
 
 
 Submitting a PR
 ---------------
-Before submitting a new pull request, please make sure you followed these instructions:
+Before submitting a new pull request, please make sure you followed these
+instructions:
 
-- make sure that your code follows the above specified conventions (see `Code style guide`_ and `Writing documentation`_).
-- if applicable, make sure you've added/modified at least 1 test to account for the changes you've made
+- make sure that your code follows the above specified conventions (see
+    `Code style guide`_ and `Writing documentation`_).
+- if applicable, make sure you've added/modified at least 1 test to account
+    for the changes you've made.
 - make sure that all tests pass locally (see `Testing`_).
-- if there is no issue which this PR solves, create a new `one <https://github.com/faridrashidi/trisicell/issues/new>`_ and briefly explaining what the problem is.
+- if there is no issue which this PR solves, create a new
+    `one <https://github.com/faridrashidi/trisicell/issues/new>`_ and briefly
+    explaining what the problem is.
 
 
 Creating a new release
 ----------------------
-If you are a core developer and you want to create a new release, you need to install ``bump2version`` first as::
+If you are a core developer and you want to create a new release, you need to
+install ``bump2version`` first as::
 
     pip install bump2version
 
 Depending on what part of the release you want to update, you can run::
 
     bump2version {major,minor,patch}
 
-By default, this will create a new tag and automatically update the ``__version__`` wherever necessary, commit the changes and create a new tag. If you have uncommitted files in the tree, you can use ``--allow-dirty`` flag to include them in the commit.
+By default, this will create a new tag and automatically update the
+``__version__`` wherever necessary, commit the changes and create a new tag.
+If you have uncommitted files in the tree, you can use ``--allow-dirty``
+flag to include them in the commit.
 
-After the version has been bumped, make sure to push the commit **AND** the newly create tag to the upstream. This can be done by e.g. setting ``push.followtags=true`` in your git config or use ``git push --atomic <branch> <tag>``.
+After the version has been bumped, make sure to push the commit **AND**
+the newly create tag to the upstream. This can be done by e.g. setting
+``push.followtags=true`` in your git config or use
+``git push --atomic <branch> <tag>``.

Makefile

@@ -1,5 +1,5 @@
 test:
-	pytest --disable-pytest-warnings --cov=trisicell ./tests
+	pytest --cov=trisicell ./tests
 	rm -rf .coverage*
 
 lint:

README.rst

@@ -1,20 +1,23 @@
-|DOI| |Stars| |PyPI| |PyPIDownloads| |Contributions Welcome| |Build Status| |Docs Status| |Pre-commit| |Code Style|
+|DOI| |Stars| |PyPI| |PyPIDownloads| |Contributions Welcome| |Build Status|
+|Docs Status| |Pre-commit| |Code Style| |Code Score|
 
 
-Trisicell - Scalable intratumor heterogeneity inference and validation from single-cell data
-============================================================================================
+Trisicell - |subst|
+===================
+
 
 .. image:: https://raw.githubusercontent.com/faridrashidi/trisicell/master/docs/source/_static/images/overview.png
    :target: https://trisicell.readthedocs.io
    :alt: overview
    :align: center
 
 
-Trisicell (**Tri**\ ple-toolkit for **si**\ ngle-\ **cell** intratumor heterogeneity inference),
-pronounced as "tricycle", is a new computational toolkit for scalable intratumor heterogeneity inference
-and evaluation from single-cell RNA, as well as single-cell genome or exome, sequencing data. Trisicell
-utilizes expressed SNVs and Indels to infer evolutionary relationships between genomic alterations
-and the cells that harbor them.
+Trisicell (**Tri**\ ple-toolkit for **si**\ ngle-\ **cell** intratumor
+heterogeneity inference), pronounced as "tricycle", is a new computational
+toolkit for scalable intratumor heterogeneity inference and evaluation from
+single-cell RNA, as well as single-cell genome or exome, sequencing data.
+Trisicell utilizes expressed SNVs and Indels to infer evolutionary
+relationships between genomic alterations and the cells that harbor them.
 
 
 Manuscript
@@ -31,15 +34,18 @@ Your help to improve Trisicell is highly appreciated.
 Trisicell was developed in collaboration between the `Cancer Data Science Laboratory (CDSL) <https://ccr.cancer.gov/cancer-data-science-laboratory>`_ and the `Laboratory of Cancer Biology and Genetics (LCBG) <https://ccr.cancer.gov/laboratory-of-cancer-biology-and-genetics>`_ at the `National Cancer Institute (NCI) <https://www.cancer.gov>`_.
 
 
+.. |subst| replace:: Scalable intratumor heterogeneity inference and validation
+                    from single-cell data
+
 .. |DOI| image:: https://img.shields.io/badge/DOI-10.1101/2021.03.26.437185-orange?style=flat-square
     :target: https://doi.org/10.1101/2021.03.26.437185
     :alt: DOI
 
-.. |PyPI| image:: https://img.shields.io/pypi/v/trisicell?style=flat-square&color=blue
+.. |PyPI| image:: https://img.shields.io/pypi/v/trisicell?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue
     :target: https://pypi.org/project/trisicell
     :alt: PyPI
 
-.. |PyPIDownloads| image:: https://img.shields.io/badge/dynamic/json?style=flat-square&color=blue&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ftrisicell
+.. |PyPIDownloads| image:: https://img.shields.io/badge/dynamic/json?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ftrisicell
     :target: https://pepy.tech/project/trisicell
     :alt: PyPIDownloads
 
@@ -51,7 +57,7 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
     :target: https://github.com/faridrashidi/trisicell/blob/master/CONTRIBUTING.rst
     :alt: Contributions Welcome
 
-.. |Build Status| image:: https://img.shields.io/github/workflow/status/faridrashidi/trisicell/CI/master?label=CI&logo=github&style=flat-square
+.. |Build Status| image:: https://img.shields.io/github/workflow/status/faridrashidi/trisicell/CI/master?label=build&logo=github&style=flat-square
     :target: https://github.com/faridrashidi/trisicell/actions?query=workflow%3ACI
     :alt: Build Status
 
@@ -67,4 +73,8 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
     :target: https://github.com/python/black
     :alt: Code Style
 
+.. |Code Score| image:: https://img.shields.io/lgtm/grade/python/github/faridrashidi/trisicell.svg?logo=lgtm&logoWidth=18&style=flat-square
+    :target: https://lgtm.com/projects/g/faridrashidi/trisicell/context:python
+    :alt: Code Style
+
 .. _preprint: https://doi.org/10.1101/2021.03.26.437185