Merge pull request #120 from KrishnaswamyLab/dev

scprep v1.1.0

.github/workflows/pre-commit.yml

@@ -0,0 +1,44 @@
+name: pre-commit
+on:
+  push:
+    branches-ignore:
+      - 'master'
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.6.0
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+          architecture: "x64"
+
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}-
+
+      - uses: pre-commit/action@v2.0.0
+        continue-on-error: true
+
+      - name: Commit files
+        run: |
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git commit -m "pre-commit" -a
+          fi
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}

.github/workflows/run_tests.yml

@@ -36,8 +36,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -U wheel setuptools
-        pip install -U black flake8
-
+        pip install -U black flake8 hacking
     - name: Lint with Black
       run: |
         black . --check --diff
@@ -56,9 +55,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - {name: 'current', os: ubuntu-latest, python: '3.8', r: 'release' }
-        - {name: 'prev', os: ubuntu-latest, python: '3.7', r: 'release' }
-        - {name: 'old', os: ubuntu-latest, python: '3.6', r: 'release' }
+        - {name: '3.9', os: ubuntu-latest, python: '3.9', r: 'release' }
+        - {name: '3.8', os: ubuntu-latest, python: '3.8', r: 'release' }
+        - {name: '3.7', os: ubuntu-latest, python: '3.7', r: 'release' }
+        - {name: '3.6', os: ubuntu-latest, python: '3.6', r: 'release' }
 
     steps:
     - name: Cancel Previous Runs
@@ -74,7 +74,7 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         sudo apt-get update -qq
-        sudo apt-get install -y pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg
+        sudo apt-get install -y pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg libhdf5-dev
 
     - name: Set up Python
       uses: actions/setup-python@v2
@@ -116,8 +116,17 @@ jobs:
         renv::restore()
         renv::install("bioc::splatter")
         renv::install("bioc::slingshot")
+        renv::install("github::dynverse/dyngen")
+        renv::install("github::dynverse/dynwrap")
       shell: Rscript {0}
 
+    - name: Install package & dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -U wheel setuptools
+        pip install -U .[test]
+        python -c "import scprep"
+
     - name: Run tests
       run: nose2 -vvv
 

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: \.(ai|gz)$
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.6.4
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+        args: ['--target-version=py36']
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.5.4
+    hooks:
+      - id: autopep8
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
+      - id: flake8
+        additional_dependencies: ['hacking']

CODE_OF_CONDUCT.md

@@ -73,4 +73,4 @@ available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.ht
 [homepage]: https://www.contributor-covenant.org
 
 For answers to common questions about this code of conduct, see
-https://www.contributor-covenant.org/faq
+https://www.contributor-covenant.org/faq

CONTRIBUTING.md

@@ -25,7 +25,7 @@ Code Style and Testing
 
 `scprep` is maintained at close to 100% code coverage. Contributors are encouraged to write tests for their code, but if you do not know how to do so, please do not feel discouraged from contributing code! Others can always help you test your contribution.
 
-Code style is dictated by [`black`](https://pypi.org/project/black/#installation-and-usage). To automatically reformat your code when you run `git commit`, you can run `./autoblack.sh` in the root directory of this project to add a hook to your `git` repository.
+Code style is dictated by [`black`](https://pypi.org/project/black/#installation-and-usage) and [`flake8`](https://flake8.pycqa.org/en/latest/) with [`hacking`](https://github.com/openstack/hacking). Code is automatically reformatted by [`pre-commit`](https://pre-commit.com/) when you push to GitHub.
 
 Code of Conduct
 ---------------

README.rst

@@ -25,6 +25,12 @@
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/psf/black
     :alt: Code style: black
+.. image:: https://img.shields.io/badge/style%20guide-openstack-eb1a32.svg
+    :target: https://docs.openstack.org/hacking/latest/user/hacking.html#styleguide
+    :alt: Style Guide: OpenStack
+.. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
+    :target: https://github.com/pre-commit/pre-commit
+    :alt: pre-commit
 
 `scprep` provides an all-in-one framework for loading, preprocessing, and plotting matrices in Python, with a focus on single-cell genomics.
 
@@ -64,7 +70,7 @@ You can use `scprep` with your single cell data as follows::
     # Filter by mitochondrial expression to remove dead cells
     mt_genes = scprep.select.get_gene_set(data, starts_with="MT")
     scprep.plot.plot_gene_set_expression(data, genes=mt_genes, percentile=90)
-    data = scprep.filter.filter_gene_set_expression(data, genes=mt_genes, 
+    data = scprep.filter.filter_gene_set_expression(data, genes=mt_genes,
                                                     percentile=90)
     # Library size normalize
     data = scprep.normalize.library_size_normalize(data)

data/test_data/gene_symbols.csv

@@ -1 +1 @@
-Arl8b,Cdc16,Lrrc8b,0610009B22Rik,Apoe,Asap1,Gstm5,Mok,Rps27l,Stap2,Prpf40a,Pam16,Rnf220,Tmem9b,Rdx,Nupr1l,4930455B14Rik,Sdf2l1,4921517D22Rik,Psmd8,Dynlrb2,Smco4,Gm14285,Ctdp1,Hnrnpu,Ldhb,Cep63,Unc50,Chd5,Ift22,Ankrd13a,Atp5o,Cdhr4,Atp1b3,Gm553,Phtf1,Fam177a,Dgkh,Atoh8,1700019G24Rik,Sycp1,1110008F13Rik,Pgam2,Ift74,Akr1cl,Adam30,Psmd12,mt-Cytb,Ccdc33,Gsto2,Gm16208,C1ql1,Loxhd1,Dhfr,Fgf13,D130052B06Rik,Pcdhb3,Krt32,4833407H14Rik,Abcc5,Vmn1r118,Ccdc54,Megf6,Gm13872,Erp44,Rgs13,Slc2a3,Gm11116,Gm16279,Trmt1,Gm7697,Gm11579,Zdhhc20,4930444P10Rik,RP23-449M8.6,Gm12631,Stoml3,Metrn,Tmco5,Fabp12,Gm3486,Hnf1aos2,Tmem200b,Olfr91,Gm19273,Hmga1-rs1,Prl3d3,Crygf,D030040B21Rik,Serpinb9e,Fam126b,Gm26873,Gm42435,Dmxl2,Cep164,Kansl2,Mgat1,Thrsp,Gm20821,Olfr203
+Arl8b,Cdc16,Lrrc8b,0610009B22Rik,Apoe,Asap1,Gstm5,Mok,Rps27l,Stap2,Prpf40a,Pam16,Rnf220,Tmem9b,Rdx,Nupr1l,4930455B14Rik,Sdf2l1,4921517D22Rik,Psmd8,Dynlrb2,Smco4,Gm14285,Ctdp1,Hnrnpu,Ldhb,Cep63,Unc50,Chd5,Ift22,Ankrd13a,Atp5o,Cdhr4,Atp1b3,Gm553,Phtf1,Fam177a,Dgkh,Atoh8,1700019G24Rik,Sycp1,1110008F13Rik,Pgam2,Ift74,Akr1cl,Adam30,Psmd12,mt-Cytb,Ccdc33,Gsto2,Gm16208,C1ql1,Loxhd1,Dhfr,Fgf13,D130052B06Rik,Pcdhb3,Krt32,4833407H14Rik,Abcc5,Vmn1r118,Ccdc54,Megf6,Gm13872,Erp44,Rgs13,Slc2a3,Gm11116,Gm16279,Trmt1,Gm7697,Gm11579,Zdhhc20,4930444P10Rik,RP23-449M8.6,Gm12631,Stoml3,Metrn,Tmco5,Fabp12,Gm3486,Hnf1aos2,Tmem200b,Olfr91,Gm19273,Hmga1-rs1,Prl3d3,Crygf,D030040B21Rik,Serpinb9e,Fam126b,Gm26873,Gm42435,Dmxl2,Cep164,Kansl2,Mgat1,Thrsp,Gm20821,Olfr203

doc/Makefile

@@ -18,4 +18,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/source/conf.py

@@ -13,14 +13,15 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+import glob
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import sys
-import glob
 import shutil
+import sys
 
 root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
 sys.path.insert(0, root_dir)
@@ -211,4 +212,4 @@
     \texttt{\strut{}{{ docname }}}\\[-0.5\baselineskip]
     \noindent\rule{\textwidth}{0.4pt}}
     \vspace{-2\baselineskip}
-"""
+"""  # noqa

doc/source/examples/index.rst

@@ -4,4 +4,4 @@ Examples
 .. toctree::
 
     scatter
-    jitter
+    jitter

requirements.txt

@@ -3,3 +3,4 @@ scipy>=0.18.1
 scikit-learn>=0.19.1
 pandas>=0.25
 decorator>=4.3.0
+packaging

scprep/__init__.py

@@ -1,20 +1,17 @@
-# author: Scott Gigante <scott.gigante@yale.edu>
-# (C) 2018 Krishnaswamy Lab GPLv2
-
+from . import _patch
 from .version import __version__
+
+import scprep.filter
 import scprep.io
 import scprep.io.hdf5
-import scprep.select
-import scprep.filter
-import scprep.normalize
-import scprep.transform
 import scprep.measure
+import scprep.normalize
 import scprep.plot
-import scprep.sanitize
-import scprep.stats
 import scprep.reduce
 import scprep.run
-
-from . import _patch
+import scprep.sanitize
+import scprep.select
+import scprep.stats
+import scprep.transform
 
 _patch.patch_fill_value()

scprep/_lazyload.py

@@ -1,10 +1,13 @@
 import importlib
 import sys
 
-# Key:
-# { module : [{submodule1:[subsubmodule1, subsubmodule2]}, submodule2] }
-# each module loads submodules on initialization but is only imported
-# and loads methods/classes when these are accessed
+"""Key:
+
+{ module : [{submodule1:[subsubmodule1, subsubmodule2]}, submodule2] }
+
+Each module loads submodules on initialization but is only imported
+and loads methods/classes when these are accessed.
+"""
 _importspec = {
     "matplotlib": [
         "colors",
@@ -31,7 +34,20 @@
 
 
 class AliasModule(object):
+    """Wrapper around Python module to allow lazy loading."""
+
     def __init__(self, name, members=None):
+        """Initialize a module without loading it.
+
+        Parameters
+        ----------
+        name : str
+            Module name
+        members : list[str, dict]
+            List of submodules to be loaded as AliasModules. If a dict, the submodule
+            is loaded with subsubmodules corresponding to the dictionary values;
+            if a string, the submodule has no subsubmodules.
+        """
         # easy access to AliasModule members to avoid recursionerror
         super_setattr = super().__setattr__
         if members is None:
@@ -56,6 +72,7 @@ def __init__(self, name, members=None):
 
     @property
     def __loaded_module__(self):
+        """Load the module, or retrieve it if already loaded."""
         # easy access to AliasModule members to avoid recursionerror
         super_getattr = super().__getattribute__
         name = super_getattr("__module_name__")
@@ -67,6 +84,7 @@ def __loaded_module__(self):
             return sys.modules[name]
 
     def __getattribute__(self, attr):
+        """Access AliasModule members."""
         # easy access to AliasModule members to avoid recursionerror
         super_getattr = super().__getattribute__
         if attr in super_getattr("__submodules__"):
@@ -85,8 +103,10 @@ def __getattribute__(self, attr):
             return getattr(super_getattr("__loaded_module__"), attr)
 
     def __setattr__(self, name, value):
-        # allows monkey-patching
-        # easy access to AliasModule members to avoid recursionerror
+        """Allow monkey-patching.
+
+        Gives easy access to AliasModule members to avoid recursionerror.
+        """
         super_getattr = super().__getattribute__
         return setattr(super_getattr("__loaded_module__"), name, value)