Repository: MDAnalysis/membrane-curvature (language: python)

Issue:
Names in repo are not consistent. 
Currently, there are two names used in the repo `MDAkit_MembCurv` and `membrane_curvature`.
For consistency, change names to `membrane_curvature`. 
Names in repo are not consistent. 
Currently, there are two names used in the repo `MDAkit_MembCurv` and `membrane_curvature`.
For consistency, change names to `membrane_curvature`. 


Discussion / hints:

Fix patch:
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 5904883..bcf5ea8 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into this mdakit_membcurv. 
+describes how to merge code changes into this membrane_curvature. 
 
 ## Getting Started
 
@@ -19,7 +19,7 @@ describes how to merge code changes into this mdakit_membcurv.
   [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
   with the branch name relating to the feature you are going to add.
 * When you are ready for others to examine and comment on your new feature,
-  navigate to your fork of mdakit_membcurv on GitHub and open a [pull
+  navigate to your fork of membrane_curvature on GitHub and open a [pull
   request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
   after you launch a PR from one of your fork's branches, all
   subsequent commits to that branch will be added to the open pull request
@@ -29,7 +29,7 @@ describes how to merge code changes into this mdakit_membcurv.
 * If you're providing a new feature, you must add test cases and documentation.
 * When the code is ready to go, make sure you run the test suite using pytest.
 * When you're ready to be considered for merging, check the "Ready to go"
-  box on the PR page to let the mdakit_membcurv devs know that the changes are complete.
+  box on the PR page to let the membrane_curvature devs know that the changes are complete.
   The code will not be merged until this box is checked, the continuous
   integration returns checkmarks,
   and multiple core developers give "Approved" reviews.
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 1ce2928..dd34bf1 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -66,7 +66,7 @@ jobs:
       shell: bash -l {0}
 
       run: |
-        pytest -v --cov=mdakit_membcurv --cov-report=xml --color=yes mdakit_membcurv/tests/
+        pytest -v --cov=membrane_curvature --cov-report=xml --color=yes membrane_curvature/tests/
 
     - name: CodeCov
       uses: codecov/codecov-action@v1
diff --git a/.lgtm.yml b/.lgtm.yml
index ecc0574..a53bf0a 100644
--- a/.lgtm.yml
+++ b/.lgtm.yml
@@ -9,4 +9,4 @@ path_classifiers:
     - versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
     - devtools/*
   generated:
-    - mdakit_membcurv/_version.py
+    - membrane_curvature/_version.py
diff --git a/MANIFEST.in b/MANIFEST.in
index 7d84433..9549ee6 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,5 +3,5 @@ include MANIFEST.in
 include CODE_OF_CONDUCT.md
 include versioneer.py
 
-graft mdakit_membcurv
+graft membrane_curvature
 global-exclude *.py[cod] __pycache__ *.so
\ No newline at end of file
diff --git a/README.md b/README.md
index cd6219c..af33b3b 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-MDA Membrane Curvature
+Membrane Curvature
 ==============================
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://www.numfocus.org/)
 [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
diff --git a/devtools/README.md b/devtools/README.md
index 148705f..9e7a994 100644
--- a/devtools/README.md
+++ b/devtools/README.md
@@ -59,5 +59,5 @@ is installed by looking at the `git` tags and how many commits ahead this versio
 \d+.\d+.\d+(?\+\d+-[a-z0-9]+)
 ```
 If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, 
-e.g. `mdakit_membcurv-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+e.g. `membrane_curvature-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
 ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash.
diff --git a/docs/Makefile b/docs/Makefile
index 6488e81..8d953c8 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = mdakit_membcurv
+SPHINXPROJ    = membrane_curvature
 SOURCEDIR     = .
 BUILDDIR      = _build
 
diff --git a/docs/README.md b/docs/README.md
index b5a5a98..5cd5884 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,4 +1,4 @@
-# Compiling MDAkit MembCurv's Documentation
+# Compiling Membrane Curvature's Documentation
 
 The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/).
 To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed.
diff --git a/docs/api.rst b/docs/api.rst
index 3f37a56..a10ef4e 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -7,4 +7,4 @@ API Documentation
 .. toctree::
 
 
-   mdakit_membcurv.canvas
+   membrane_curvature.canvas
diff --git a/docs/conf.py b/docs/conf.py
index dda7a69..3edb791 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -13,16 +13,15 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
 # Incase the project was not installed
+import membrane_curvature
 import os
 import sys
 sys.path.insert(0, os.path.abspath('..'))
 
-import mdakit_membcurv
-
 
 # -- Project information -----------------------------------------------------
 
-project = 'MDAkit_membcurv'
+project = 'membrane_curvature'
 copyright = ("2021, Estefania Barreto-Ojeda. Project structure based on the "
              "Computational Molecular Science Python Cookiecutter version 1.5")
 author = 'Estefania Barreto-Ojeda'
@@ -117,7 +116,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mdakit_membcurvdoc'
+htmlhelp_basename = 'membrane_curvaturedoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -144,8 +143,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'mdakit_membcurv.tex', 'MDAkit MembCurv Documentation',
-     'mdakit_membcurv', 'manual'),
+    (master_doc, 'membrane_curvature.tex', 'Membrane Curvature Documentation',
+     'membrane_curvature', 'manual'),
 ]
 
 
@@ -154,7 +153,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'mdakit_membcurv', 'MDAkit MembCurv Documentation',
+    (master_doc, 'membrane_curvature', 'Membrane Curvature Documentation',
      [author], 1)
 ]
 
@@ -165,8 +164,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'mdakit_membcurv', 'MDAkit MembCurv Documentation',
-     author, 'mdakit_membcurv', 'MDAkit for Membrane Curvature',
+    (master_doc, 'membrane_curvature', 'Membrane Curvature Documentation',
+     author, 'membrane_curvature', 'MDAkit for Membrane Curvature',
      'Miscellaneous'),
 ]
 
diff --git a/docs/index.rst b/docs/index.rst
index 70f79f7..33d70a8 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,9 +1,9 @@
-.. mdakit_membcurv documentation master file, created by
+.. membrane_curvature documentation master file, created by
    sphinx-quickstart on Thu Mar 15 13:55:56 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to MDAkit MembCurv's documentation!
+Welcome to Membrane Curvature's documentation!
 =========================================================
 
 The MDAnalysis membrane curvature analysis module calculates the Gaussian and mean 
diff --git a/mdakit_membcurv/__init__.py b/membrane_curvature/__init__.py
similarity index 94%
rename from mdakit_membcurv/__init__.py
rename to membrane_curvature/__init__.py
index 861ebb1..38923a2 100644
--- a/mdakit_membcurv/__init__.py
+++ b/membrane_curvature/__init__.py
@@ -1,5 +1,5 @@
 """
-MDAkit MembCurv
+
 MDAkit for Membrane Curvature
 """
 
diff --git a/mdakit_membcurv/_version.py b/membrane_curvature/_version.py
similarity index 99%
rename from mdakit_membcurv/_version.py
rename to membrane_curvature/_version.py
index c5ca315..35b5c3c 100644
--- a/mdakit_membcurv/_version.py
+++ b/membrane_curvature/_version.py
@@ -43,7 +43,7 @@ def get_config():
     cfg.style = "pep440"
     cfg.tag_prefix = ""
     cfg.parentdir_prefix = "None"
-    cfg.versionfile_source = "mdakit_membcurv/_version.py"
+    cfg.versionfile_source = "membrane_curvature/_version.py"
     cfg.verbose = False
     return cfg
 
diff --git a/mdakit_membcurv/core.py b/membrane_curvature/core.py
similarity index 100%
rename from mdakit_membcurv/core.py
rename to membrane_curvature/core.py
diff --git a/mdakit_membcurv/data/README.md b/membrane_curvature/data/README.md
similarity index 100%
rename from mdakit_membcurv/data/README.md
rename to membrane_curvature/data/README.md
diff --git a/mdakit_membcurv/data/look_and_say.dat b/membrane_curvature/data/look_and_say.dat
similarity index 100%
rename from mdakit_membcurv/data/look_and_say.dat
rename to membrane_curvature/data/look_and_say.dat
diff --git a/mdakit_membcurv/lib/mods.py b/membrane_curvature/lib/mods.py
similarity index 100%
rename from mdakit_membcurv/lib/mods.py
rename to membrane_curvature/lib/mods.py
diff --git a/setup.cfg b/setup.cfg
index 05957c1..d8c7c2e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -6,7 +6,7 @@ omit =
     # Omit the tests
     */tests/*
     # Omit generated versioneer
-    mdakit_membcurv/_version.py
+    membrane_curvature/_version.py
 
 [yapf]
 # YAPF, in .style.yapf files this shows up as "[style]" header
@@ -22,8 +22,8 @@ max-line-length = 119
 # Automatic version numbering scheme
 VCS = git
 style = pep440
-versionfile_source = mdakit_membcurv/_version.py
-versionfile_build = mdakit_membcurv/_version.py
+versionfile_source = membrane_curvature/_version.py
+versionfile_build = membrane_curvature/_version.py
 tag_prefix = ''
 
 [aliases]
diff --git a/setup.py b/setup.py
index f314c78..cfa1629 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
 """
-MDAkit MembCurv
+
 MDAkit for Membrane Curvature
 """
 import sys
@@ -21,8 +21,8 @@
 
 setup(
     # Self-descriptive entries which should always be present
-    name='mdakit_membcurv',
-    author='MDAnalysis',
+    name='membrane_curvature',
+    author='Estefania Barreto-Ojeda',
     author_email='estefania.b.ojeda@gmail.com',
     description=short_description[0],
     long_description=long_description,


Test patch:
diff --git a/mdakit_membcurv/data/test_curvature_abca1.gro b/membrane_curvature/data/test_curvature_abca1.gro
similarity index 100%
rename from mdakit_membcurv/data/test_curvature_abca1.gro
rename to membrane_curvature/data/test_curvature_abca1.gro
diff --git a/mdakit_membcurv/data/test_curvature_abca1.xtc b/membrane_curvature/data/test_curvature_abca1.xtc
similarity index 100%
rename from mdakit_membcurv/data/test_curvature_abca1.xtc
rename to membrane_curvature/data/test_curvature_abca1.xtc
diff --git a/mdakit_membcurv/data/test_curvature_po4_only.gro b/membrane_curvature/data/test_curvature_po4_only.gro
similarity index 100%
rename from mdakit_membcurv/data/test_curvature_po4_only.gro
rename to membrane_curvature/data/test_curvature_po4_only.gro
diff --git a/mdakit_membcurv/data/test_curvature_po4_only.xtc b/membrane_curvature/data/test_curvature_po4_only.xtc
similarity index 100%
rename from mdakit_membcurv/data/test_curvature_po4_only.xtc
rename to membrane_curvature/data/test_curvature_po4_only.xtc
diff --git a/mdakit_membcurv/tests/__init__.py b/membrane_curvature/tests/__init__.py
similarity index 100%
rename from mdakit_membcurv/tests/__init__.py
rename to membrane_curvature/tests/__init__.py
diff --git a/mdakit_membcurv/tests/datafiles.py b/membrane_curvature/tests/datafiles.py
similarity index 93%
rename from mdakit_membcurv/tests/datafiles.py
rename to membrane_curvature/tests/datafiles.py
index 767ca98..b8561fa 100644
--- a/mdakit_membcurv/tests/datafiles.py
+++ b/membrane_curvature/tests/datafiles.py
@@ -6,7 +6,7 @@
 
 MD simulations files stored in `data` sub-directory.
 
-    from mdakit_membcurv.datafiles import *
+    from membrane_curvature.datafiles import *
 """
 
 __all__ = [
diff --git a/mdakit_membcurv/tests/test_mdakit_membcurv.py b/membrane_curvature/tests/test_mdakit_membcurv.py
similarity index 98%
rename from mdakit_membcurv/tests/test_mdakit_membcurv.py
rename to membrane_curvature/tests/test_mdakit_membcurv.py
index 7d7f4c2..b030bbc 100644
--- a/mdakit_membcurv/tests/test_mdakit_membcurv.py
+++ b/membrane_curvature/tests/test_mdakit_membcurv.py
@@ -1,5 +1,5 @@
 """
-Unit and regression test for the mdakit_membcurv package.
+Unit and regression test for the membrane_curvature package.
 """
 
 # Import package, test suite, and other packages as needed
@@ -15,7 +15,7 @@
 import numpy as np
 from numpy.testing import assert_almost_equal
 import MDAnalysis as mda
-from mdakit_membcurv.tests.datafiles import GRO_MEMBRANE_PROTEIN, XTC_MEMBRANE_PROTEIN, GRO_PO4, XTC_PO4
+from membrane_curvature.tests.datafiles import GRO_MEMBRANE_PROTEIN, XTC_MEMBRANE_PROTEIN, GRO_PO4, XTC_PO4
 
 # Reference data from datafile
 MEMBRANE_CURVATURE_DATA = {
@@ -188,9 +188,9 @@ def md_ref_beads():
     return md_ref_beads
 
 
-def test_mdakit_membcurv_imported():
+def test_membrane_curvature_imported():
     """Sample test, will always pass so long as import statement worked"""
-    assert "mdakit_membcurv" in sys.modules
+    assert "membrane_curvature" in sys.modules
 
 
 def test_dict_to_pickle(tmpdir):