rename sencha to orpheum

Author: pranathivemuri

.github/pull_request_template.md

@@ -1,4 +1,4 @@
-Many thanks to contributing to czbiohub/sencha!
+Many thanks to contributing to czbiohub/orpheum!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
 

.gitignore

@@ -1,7 +1,7 @@
 *.py[cod]
 
 # autogenerated versioning file
-sencha/version.py
+orpheum/version.py
 
 # C extensions
 *.so

CONTRIBUTING.md

@@ -10,7 +10,7 @@ Types of Contributions
 
 ### Report Bugs
 
-Report bugs at <https://github.com/>czbiohub/sencha/issues.
+Report bugs at <https://github.com/>czbiohub/orpheum/issues.
 
 If you are reporting a bug, please include:
 
@@ -34,7 +34,7 @@ even on the web in blog posts, articles, and such.
 
 ### Submit Feedback
 
-The best way to send feedback is to file an issue at <https://github.com/>czbiohub/sencha/issues.
+The best way to send feedback is to file an issue at <https://github.com/>czbiohub/orpheum/issues.
 
 If you are proposing a feature:
 
@@ -45,18 +45,18 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up sencha for
+Ready to contribute? Here's how to set up orpheum for
 local development.
 
-1.  Fork the sencha repo on GitHub.
+1.  Fork the orpheum repo on GitHub.
 2.  Clone your fork locally:
 
-        $ git clone [email protected]:your_name_here/sencha.git
+        $ git clone [email protected]:your_name_here/orpheum.git
 
 3.  Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
 
-        $ mkvirtualenv sencha
-        $ cd sencha/
+        $ mkvirtualenv orpheum
+        $ cd orpheum/
         $ python setup.py develop
 
 4.  Create a branch for local development:
@@ -72,7 +72,7 @@ local development.
         $ py.test
         $ tox
 
-    To get black and tox, just pip install them into your virtualenv. Note: run formatting commands from the top sencha directory.
+    To get black and tox, just pip install them into your virtualenv. Note: run formatting commands from the top orpheum directory.
 
 6.  Commit your changes and push your branch to GitHub:
 
@@ -90,7 +90,7 @@ Before you submit a pull request, check that it meets these guidelines:
 1.  The pull request should include tests.
 2.  If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
 3.  The pull request should work for Python 3.6 and 3.7. Check
-    <https://travis-ci.org/>czbiohub/sencha/pull\_requests and make sure that the tests pass
+    <https://travis-ci.org/>czbiohub/orpheum/pull\_requests and make sure that the tests pass
     for all supported Python versions.
 
 Tips

MANIFEST.in

@@ -1,6 +1,6 @@
 include LICENSE Makefile README.md HISTORY.md CONTRIBUTING.md AUTHORS.md requirements.txt
 
-recursive-include sencha/tests *
+recursive-include orpheum/tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 

Makefile

@@ -8,14 +8,14 @@ test:
 	py.test
 
 coverage:
-	coverage run --source sencha --omit="*/test*" --module py.test
+	coverage run --source orpheum --omit="*/test*" --module py.test
 	coverage report --show-missing
 
 lint:
 	# ignore:
 	# E126 continuation line over-indented for hanging indent
 	# E127 continuation line over-indented for visual indent
-	flake8 --exclude docs,tests --ignore=E127,E126 sencha
+	flake8 --exclude docs,tests --ignore=E127,E126 orpheum
 
 conda_install:
 	conda install --file conda_requirements.txt

README.md

@@ -1,37 +1,33 @@
-sencha
+orpheum
 ================================
-![Tests](https://github.com/czbiohub/sencha/workflows/Pytest/badge.svg)
-![Linting](https://github.com/czbiohub/sencha/workflows/Lint%20with%20flake8/badge.svg)
-[![codecov](https://codecov.io/gh/czbiohub/sencha/branch/master/graph/badge.svg)](https://codecov.io/gh/czbiohub/sencha)
+![Tests](https://github.com/czbiohub/orpheum/workflows/Pytest/badge.svg)
+![Linting](https://github.com/czbiohub/orpheum/workflows/Lint%20with%20flake8/badge.svg)
+[![codecov](https://codecov.io/gh/czbiohub/orpheum/branch/master/graph/badge.svg)](https://codecov.io/gh/czbiohub/orpheum)
 
-What is sencha?
+What is orpheum?
 -------------------------------------
 
 Sencha is a Python package for directly translating RNA-seq reads into coding protein sequence.
 
 -   Free software: MIT license
--   Documentation: https://czbiohub.github.io/sencha
-
-The name is inspired from the naming pattern of [sourmash](https://github.com/dib-lab/sourmash)
-combined with [@olgabot](https://github.com/olgabot/)'s love of tea.
-([Sencha](https://en.wikipedia.org/wiki/Sencha) is a Japanese green tea.)
+-   Documentation: https://czbiohub.github.io/orpheum
 
 Installation
 ------------
 
 The package can be installed from PyPI using `pip` here:
 
 ```
-pip install sencha
+pip install orpheum
 ```
 
 ### Developmental install
 
 To install this code and play around with the code locally, clone this github repository and use `pip` to install:
 
 ```
-git clone https://github.com/czbiohub/sencha.git
-cd sencha
+git clone https://github.com/czbiohub/orpheum.git
+cd orpheum
 
 # The "." means "install *this*, the folder where I am now"
 pip install .
@@ -45,7 +41,7 @@ Usage
 A reference proteome *must* be supplied as the first argument.
 
 ```
-sencha translate reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 
 #### Save the "coding scores" to a csv or parquet file
@@ -59,12 +55,12 @@ see the coding scores for all reads, use the `--csv` flag or `--parquet` flag.
 
 csv:
 ```
-sencha translate --csv coding_scores.csv reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate --csv coding_scores.csv reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 
 parquet:
 ```
-sencha translate --parquet coding_scores.parquet reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate --parquet coding_scores.parquet reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 
 #### Save the coding nucleotides to a fasta
@@ -73,7 +69,7 @@ By default, only the coding *peptides* are output. If you'd like to also output
 the underlying *nucleotide* sequence, then use the flag `--coding-nucleotide-fasta`
 
 ```
-sencha translate --coding-nucleotide-fasta coding_nucleotides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate --coding-nucleotide-fasta coding_nucleotides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 
 #### Save the *non*-coding nucleotides to a fasta
@@ -82,7 +78,7 @@ To see the sequence of reads which were deemed non-coding, use the flag
 `--noncoding-nucleotide-fasta`.
 
 ```
-sencha translate --noncoding-nucleotide-fasta noncoding_nucleotides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate --noncoding-nucleotide-fasta noncoding_nucleotides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 
 #### Save the low complexity nucleotides to a fasta
@@ -98,7 +94,7 @@ would be considered low complexity. While this sequence has many nucleotide
 k-mers, it is likely a result of a sequencing error and we ignore it.
 
 ```
-sencha translate --low-complexity-nucleotide-fasta low_complexity_nucleotides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate --low-complexity-nucleotide-fasta low_complexity_nucleotides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 
 #### Save the low complexity peptides to a fasta
@@ -121,6 +117,6 @@ sequence of low-complexity peptides to a fasta, use the flag
 `--low-complexity-peptides-fasta`.
 
 ```
-sencha translate --low-complexity-peptides-fasta low_complexity_peptides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
+orpheum translate --low-complexity-peptides-fasta low_complexity_peptides.fasta reference-proteome.fa.gz *.fastq.gz > coding_peptides.fasta
 ```
 

docs/Makefile

@@ -48,7 +48,7 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)
-	rm -rf sencha*.rst
+	rm -rf orpheum*.rst
 	rm -rf modules.rst
 	rm -rf tutorial/*.rst
 	rm -rf tutorial/*_files
@@ -60,7 +60,7 @@ clean:
 html:
 	cp ../examples/*.ipynb tutorial/;
 	cd tutorial ; make notebooks ; cd ..
-	sphinx-apidoc -l -d 4 -e --force -o . ../sencha
+	sphinx-apidoc -l -d 4 -e --force -o . ../orpheum
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

docs/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# sencha documentation build configuration file, created by
+# orpheum documentation build configuration file, created by
 # sphinx-quickstart on Tue Jul  9 22:26:36 2013.
 #
 # This file is execfile()d with the current directory set to its
@@ -31,7 +31,7 @@
 # version is used.
 sys.path.insert(0, project_root)
 
-import sencha
+import orpheum
 
 # -- General configuration ---------------------------------------------
 
@@ -63,9 +63,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = sencha.__version__
+version = orpheum.__version__
 # The full version, including alpha/beta/rc tags.
-release = sencha.__version__
+release = orpheum.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -188,7 +188,7 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "senchadoc"
+htmlhelp_basename = "orpheumdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -208,8 +208,8 @@
 latex_documents = [
     (
         "index",
-        "sencha.tex",
-        u"sencha Documentation",
+        "orpheum.tex",
+        u"orpheum Documentation",
         u"Chan Zuckerberg Biohub",
         "manual",
     ),
@@ -241,7 +241,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ("index", "sencha", u"Sencha Documentation", [u"Chan Zuckerberg Biohub"], 1)
+    ("index", "orpheum", u"Sencha Documentation", [u"Chan Zuckerberg Biohub"], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -256,10 +256,10 @@
 texinfo_documents = [
     (
         "index",
-        "sencha",
+        "orpheum",
         u"Sencha Documentation",
         u"Chan Zuckerberg Biohub",
-        "sencha",
+        "orpheum",
         "Sencha is a Python package for directly translating RNA-seq reads into coding protein sequence.",
         "Miscellaneous",
     ),

docs/index.rst

@@ -1,4 +1,4 @@
-.. sencha documentation master file, created by
+.. orpheum documentation master file, created by
    sphinx-quickstart on Tue Jul  9 22:26:36 2013.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/installation.rst

@@ -4,9 +4,9 @@ Installation
 
 At the command line::
 
-    $ easy_install sencha
+    $ easy_install orpheum
 
 Or, if you have virtualenvwrapper installed::
 
-    $ mkvirtualenv sencha
-    $ pip install sencha
+    $ mkvirtualenv orpheum
+    $ pip install orpheum

docs/tutorial.rst

@@ -1,6 +1,6 @@
 .. _tutorial:
 
-sencha Tutorial
+orpheum Tutorial
 =================
 
 Installation

docs/usage.md

@@ -2,21 +2,21 @@
 Usage
 ========
 
-To use sencha in a project::
+To use orpheum in a project::
 
-    import sencha
+    import orpheum
 
 To create a protein index::
 
-    sencha index --molecule protein --peptide-ksize 7 --save-as Homo_sapiens.GRCh38.pep.subset.molecule-protein_ksize-7.bloomfilter.nodegraph Homo_sapiens.GRCh38.pep.subset.fa.gz
+    orpheum index --molecule protein --peptide-ksize 7 --save-as Homo_sapiens.GRCh38.pep.subset.molecule-protein_ksize-7.bloomfilter.nodegraph Homo_sapiens.GRCh38.pep.subset.fa.gz
 
 To translate RNA-seq reads into coding peptides using the protein index::
 
-    sencha translate -- SRR306838_GSM752691_hsa_br_F_1_trimmed_subsampled.fq.gz Homo_sapiens.GRCh38.pep.all.fa.gz
+    orpheum translate -- SRR306838_GSM752691_hsa_br_F_1_trimmed_subsampled.fq.gz Homo_sapiens.GRCh38.pep.all.fa.gz
 
 To create the index and translate the reads in one step::
 
-    sencha partition  ~/code/kmer-hashing/extract_kmers/test-data/SRR306838_GSM752691_hsa_br_F_1_trimmed_subsampled.fq.gz ~/Downloads/Homo_sapiens.GRCh38.pep.all.fa.gz
+    orpheum partition  ~/code/kmer-hashing/extract_kmers/test-data/SRR306838_GSM752691_hsa_br_F_1_trimmed_subsampled.fq.gz ~/Downloads/Homo_sapiens.GRCh38.pep.all.fa.gz