Merge pull request #94 from faridrashidi/develop

release v0.0.20
faridrashidi · Nov 23, 2021 · 4db89ed · 4db89ed
2 parents 6f69784 + e99cb3b
commit 4db89ed
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.19
+current_version = 0.0.20
 commit = True
 message = [skip ci] {current_version} → {new_version}
 tag = False

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
 -   repo: https://github.com/psf/black
-    rev: 21.9b0
+    rev: 21.11b1
     hooks:
     -   id: black
         additional_dependencies: [toml]
         args: [--line-length=88, --experimental-string-processing]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.9.3
+    rev: 5.10.1
     hooks:
     -   id: isort
         additional_dependencies: [toml]
@@ -50,12 +50,12 @@ repos:
     hooks:
     -   id: rstcheck
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.11.0
+    rev: v1.12.0
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==20.8b1]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.0
+    rev: v2.29.1
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]
@@ -69,7 +69,7 @@ repos:
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
 -   repo: https://github.com/PyCQA/doc8
-    rev: 0.9.1
+    rev: 0.10.1
     hooks:
     -   id: doc8
         args: [--max-line-length=88]
@@ -85,7 +85,7 @@ repos:
         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: v1.2.3
+    rev: v1.3.0
     hooks:
     -   id: yesqa
         additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-comprehensions, flake8-bugbear, flake8-blind-except]

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,7 +1,7 @@
 prune docs
 prune .scripts
 prune .github
+include LICENSE
 include requirements.txt
 include docs/requirements.txt
-include LICENSE
 include trisicell/datasets/*
diff --git a/README.rst b/README.rst
@@ -57,7 +57,7 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
     :target: https://github.com/faridrashidi/trisicell
     :alt: Stars
 
-.. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions&message=welcome&color=0059b3&logo=handshake&logoColor=FFFFFF&style=flat-square
+.. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions&message=welcome&color=blue&logo=handshake&logoColor=FFFFFF&style=flat-square
     :target: https://github.com/faridrashidi/trisicell/blob/master/CONTRIBUTING.rst
     :alt: Contributions Welcome
 
@@ -73,8 +73,8 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
     :target: https://trisicell.readthedocs.io
     :alt: Docs Status
 
-.. |Pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=flat-square
-    :target: https://github.com/pre-commit/pre-commit
+.. |Pre-commit| image:: https://img.shields.io/badge/pre--commit.ci-passing-brightgreen?logo=pre-commit&logoColor=white&style=flat-square
+    :target: https://results.pre-commit.ci/latest/github/faridrashidi/trisicell/master
     :alt: Pre-commit
 
 .. |Code Style| image:: https://img.shields.io/badge/code%20style-black-000000.svg?logo=visualstudiocode&logoColor=FFFFFF&style=flat-square

diff --git a/docs/source/about.rst b/docs/source/about.rst
@@ -59,10 +59,10 @@ observed data.
 
 There are several techniques and methods to remove the noise/conflicts from
 the input genotype matrix. They are mostly based on Integer Linear Programming
-(ILP), Constraint Satisfaction Prgramming (CSP), Markov chain Monte Carlo (MCMC)
+(ILP), Constraint Satisfaction Programming (CSP), Markov chain Monte Carlo (MCMC)
 sampling and Neighbor Joining (NJ). For more details, we highly recommend to
 read our `Trisicell <https://doi.org/10.1101/2021.03.26.437185>`_ and
-`review <https://doi.org/10.1101/2020.07.15.204081>`_ papers about building
+`review <https://doi.org/10.1089/cmb.2020.0595>`_ papers about building
 tumor progression tree by exploring the space of binary matrices.
 
 Trisicell Components

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -13,41 +13,6 @@ After mutation calling and building the input data via our suggested
 :ref:`mutation calling pipeline <caller>`.
 
 
-Datasets (datasets)
--------------------
-This module offers a bunch of functions for simulating data.
-
-.. module:: trisicell.datasets
-.. currentmodule:: trisicell
-.. autosummary::
-    :toctree: .
-
-    datasets.example
-    datasets.simulate
-    datasets.add_noise
-    datasets.melanoma20
-    datasets.colorectal1
-    datasets.colorectal2
-    datasets.colorectal3
-    datasets.acute_lymphocytic_leukemia1
-    datasets.acute_lymphocytic_leukemia2
-    datasets.acute_lymphocytic_leukemia3
-    datasets.acute_lymphocytic_leukemia4
-    datasets.acute_lymphocytic_leukemia5
-    datasets.acute_lymphocytic_leukemia6
-    datasets.high_grade_serous_ovarian_cancer1
-    datasets.high_grade_serous_ovarian_cancer2
-    datasets.high_grade_serous_ovarian_cancer3
-    datasets.high_grade_serous_ovarian_cancer_3celllines
-    datasets.myeloproliferative_neoplasms18
-    datasets.myeloproliferative_neoplasms78
-    datasets.myeloproliferative_neoplasms712
-    datasets.renal_cell_carcinoma
-    datasets.muscle_invasive_bladder
-    datasets.erbc
-    datasets.tnbc
-
-
 Read/Write (io)
 ---------------
 This module offers a bunch of functions for reading and writing of the data.
@@ -75,7 +40,6 @@ data.
     pp.remove_cell_by_list
     pp.filter_mut_reference_must_present_in_at_least
     pp.filter_mut_mutant_must_present_in_at_least
-    pp.bifiltering
     pp.consensus_combine
 
 
@@ -93,12 +57,6 @@ and calculating the probability of mutations seeding particular cells.
     :toctree: .
 
     tl.booster
-    tl.scite
-    tl.phiscsb
-    tl.scistree
-    tl.onconem
-    tl.huntress
-
 
 **Partition function calculation (Trisicell-PartF)**
 
@@ -114,20 +72,6 @@ and calculating the probability of mutations seeding particular cells.
 
     tl.consensus
 
-**For comparing two phylogenetic trees**
-
-.. autosummary::
-    :toctree: .
-
-    tl.ad
-    tl.dl
-    tl.mltd
-    tl.tpted
-    tl.caset
-    tl.disc
-    tl.mp3
-    tl.rf
-
 
 Plotting (pl)
 -------------
@@ -154,5 +98,15 @@ This module offers a bunch of utility functions.
     ul.to_tree
     ul.to_cfmatrix
     ul.to_mtree
-    ul.hclustering
-    ul.is_conflict_free_gusfield
+
+
+Datasets (datasets)
+-------------------
+This module offers a bunch of functions for simulating data.
+
+.. module:: trisicell.datasets
+.. currentmodule:: trisicell
+.. autosummary::
+    :toctree: .
+
+    datasets.example
diff --git a/docs/source/cli.rst b/docs/source/cli.rst
@@ -13,26 +13,19 @@ following output:
 
     Usage: trisicell [OPTIONS] COMMAND [ARGS]...
 
-      Scalable intratumor heterogeneity inference and validation from single-cell data
+      Trisicell.
+
+      Scalable intratumor heterogeneity inference and validation from single-cell data.
 
     Options:
       --version  Show the version and exit.
       --help     Show this message and exit.
 
     Commands:
       mcalling   Mutation calling.
-      score      Calculate scores between two trees.
-      scistree   Run ScisTree.
-      scite      Run SCITE.
-      booster    Run Booster.
-      phiscsb    Run PhISCS (CSP version).
-      phiscsi    Run PhISCS (ILP version).
-      bnb        Run PhISCS-BnB.
-      huntress   Run HUNTRESS.
-      cf2newick  Convert conflict-free to newick file.
-      cf2tree    Convert conflict-free to clonal tree.
-      consensus  Calculate consensus betweeen two trees.
-      search     Grid search for all parameters.
+      booster    Boost available tree reconstruction tool (Trisicell-Boost).
+      partf      Get samples or calculate for PartF.
+      consensus  Build consensus tree between two phylogenetic trees (Trisicell-Cons).
 
 
 ``mcalling`` - Run Mutation Calling
@@ -53,19 +46,10 @@ following output:
     :nested: full
 
 
-``scite`` - Run SCITE
----------------------
-
-.. click:: trisicell.commands.trisicell:cli
-    :prog: trisicell
-    :commands: scite
-    :nested: full
-
-
-``score`` - Calculating Scores
-------------------------------
+``consensus`` - Run Consensus
+-----------------------------
 
 .. click:: trisicell.commands.trisicell:cli
     :prog: trisicell
-    :commands: score
+    :commands: consensus
     :nested: full
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -206,7 +206,6 @@ def reset_matplotlib(gallery_conf, fname):
     "subsection_order": ExplicitOrder(
         [
             rel_example_dir / "reconstruction",  # really must be relative
-            rel_example_dir / "comparison",
         ]
     ),
     "reference_url": {

diff --git a/docs/source/release_notes.rst b/docs/source/release_notes.rst
@@ -7,6 +7,15 @@ Release Notes
 =============
 
 
+Version 0.0.20 :small:`November 22, 2021`
+-----------------------------------------
+
+This version includes:
+
+    - Add multi-threaded ScisTree.
+    - Update the documentations.
+
+
 Version 0.0.19 :small:`October 18, 2021`
 ----------------------------------------
 

diff --git a/examples/comparison/README.rst b/examples/comparison/README.rst
diff --git a/examples/comparison/compute_scores.py b/examples/comparison/compute_scores.py
diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
     __author__ = ", ".join(["Farid Rashidi"])
     __maintainer__ = ", ".join(["Farid Rashidi"])
     __email__ = ", ".join(["[email protected]"])
-    __version__ = "0.0.19"
+    __version__ = "0.0.20"
 
 if platform == "linux" or platform == "linux2":
     os.environ["CC"] = "g++"