Merge pull request #67 from rasbt/v0.2.6

V0.2.6

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,78 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity, and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language;
+* Being respectful of differing viewpoints and experiences;
+* Gracefully accepting constructive criticism;
+* Focusing on what is best for the community;
+* Showing empathy towards other community members.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances;
+* Trolling, gaslighting, insulting/derogatory comments, and personal or political attacks;
+* Public or private harassment;
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission;
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting.
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within the project and public spaces
+when an individual represents the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or other unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality concerning the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

.github/ISSUE_TEMPLATE/BUG_REPORT.md

@@ -0,0 +1,86 @@
+---
+name: Bug report
+about: Report and reproduce a bug
+title: ''
+labels: 'Bug'
+assignees: ''
+
+---
+
+<!-- 
+If this is your first Issue submitted to the BioPandas Issue Tracker, please review
+the code of conduct, which is available at http://rasbt.github.io/biopandas/Code-of-Conduct/. 
+-->
+
+
+<!--
+Before submitting a bug, please check the recent Changelog entries at 
+https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md
+and do a quick search in the Issue Tracker (https://github.com/rasbt/biopandas/issues)
+to make sure the issue hasn't been already
+addressed.
+-->
+
+#### Describe the bug
+
+<!--
+Briefly describe what the bug is.
+-->
+
+#### Steps/Code to Reproduce
+
+<!--
+
+
+<!--
+Please add a minimal example that can help understand and reproduce the bug.
+Ideally, this should be a self-contained code example that can be run
+on our computer with easily accessible datasets (ideally, datasets contained
+in scikit-learn or BioPandas itself).
+
+
+Example:
+
+```python
+import numpy as np
+from biopandas.evaluate import bootstrap
+
+
+rng = np.random.RandomState(123)
+x = rng.normal(loc=5., size=100)
+original, std_err, ci_bounds = bootstrap(x, num_rounds=1000, func=np.mean, ci=0.95, seed=123)
+print('Mean: %.2f, SE: +/- %.2f, CI95: [%.2f, %.2f]' % (original, 
+ std_err, 
+ ci_bounds[0],
+ ci_bounds[1]))
+```
+
+If the code is too long, feel free to put it in a public gist and link
+it in the issue: https://gist.github.com
+-->
+
+```python
+Insert your example code here.
+```
+
+#### Expected Results
+
+<!-- Please paste or describe the expected results.-->
+
+#### Actual Results
+<!-- Please paste or specifically describe the actual output or error traceback. -->
+
+#### Versions
+
+<!--
+Please run the following snippet and paste the output below.
+import biopandas; print("biopandas", biopandas.__version__)
+import platform; print(platform.platform())
+import sys; print("Python", sys.version)
+import sklearn; print("Scikit-learn", sklearn.__version__)
+import numpy; print("NumPy", numpy.__version__)
+import scipy; print("SciPy", scipy.__version__)
+-->
+
+
+<!-- Thanks for contributing! -->

.github/ISSUE_TEMPLATE/DOCUMENTATION_IMPROVEMENT.md

@@ -0,0 +1,26 @@
+---
+name: Documentation improvement
+about: Issues or confusions regarding the documentation
+title: ''
+labels: Documentation
+assignees: ''
+
+---
+
+<!-- 
+If this is your first Issue submitted to the BioPandas Issue Tracker, please review
+the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/. 
+-->
+
+
+#### Describe the documentation issue
+
+<!--
+Tell us about the confusion introduced in the documentation.
+-->
+
+#### Suggest a potential improvement or addition
+
+<!--
+Tell us how we could improve the documentation in this regard.
+-->

.github/ISSUE_TEMPLATE/FEATURE_REQUEST.md

@@ -0,0 +1,22 @@
+---
+name: Feature request
+about: Suggest a new algorithm, enhancement to an existing algorithm, etc.
+title: ''
+labels: New Feature
+assignees: ''
+
+---
+
+<!-- 
+If this is your first Issue submitted to the BioPandas Issue Tracker, please review
+the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/. 
+-->
+
+
+#### Describe the workflow you want to enable
+
+#### Describe your proposed solution
+
+#### Describe alternatives you've considered, if relevant
+
+#### Additional context

.github/ISSUE_TEMPLATE/OTHER.md

@@ -0,0 +1,13 @@
+---
+name: Other
+about: Issues that don't fall into any of the other categories
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+<!-- 
+If this is your first Issue submitted to the BioPandas Issue Tracker, please review
+the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/. 
+-->

.github/ISSUE_TEMPLATE/USAGE_QUESTION.md

@@ -0,0 +1,13 @@
+---
+name: Usage question
+about: If you have a usage question
+title: ''
+labels: Question
+assignees: ''
+
+---
+
+<!-- 
+If this is your first Issue submitted to the BioPandas Issue Tracker, please review
+the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/. 
+-->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,45 +1,39 @@
-<!-- Please read the following guidelines for new Pull Requests -- thank you! -->
+### Code of Conduct
 
-<!--
-Make sure that you submit this pull request as a separate topic branch (and not to "master")
+<!-- 
+If this is your first Pull Request for the BioPandas repository, please review
+the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/. 
 -->
 
-<!-- Provide a small summary describing the Pull Request below -->
 
 ### Description
 
-Insert Description Here
+<!-- 
+Please insert a brief description of the Pull request below.
+-->
 
 ### Related issues or pull requests
 
-<!-- Please provide a link to the respective issue on the [Issue Tracker](https://github.com/rasbt/biopandas/issues) if one exists. E.g.,
-
-Fixes #<ISSUE_NUMBER> -->
-
-Link related issues/pull requests here
-
-<!-- Below is a general todo list for typical pull request -->
+<!-- 
+If applicable, please link related issues/pull request below. For example, 
+"Fixes #366". Note that the "Fixes" keyword in GitHub will automatically
+close the listed issue upon merging this Pull Request.
+-->
 
-### Pull Request requirements
+### Pull Request Checklist
 
-For new features or bug fixes, pleas consider the following to-do list:
+<!--
+Please fill out the following checklist if applicable. For more more information and help, please see the Contributor Documentation avaialable at http://rasbt.github.io/biopandas/contributing/.
+-->
 
-- [ ] Added appropriate unit test functions in the `./biopandas/*/tests` directories
-- [ ] Ran `nosetests ./biopandas -sv` and make sure that all unit tests pass
-- [ ] Checked the test coverage by running `nosetests ./biopandas --with-coverage`
+- [ ] Added a note about the modification or contribution to the `./docs/sources/CHANGELOG.md` file (if applicable)
+- [ ] Added appropriate unit test functions in the `./biopandas/*/tests` directories (if applicable)
+- [ ] Modify documentation in the corresponding Jupyter Notebook under `biopandas/docs/sources/` (if applicable)
+- [ ] Ran `PYTHONPATH='.' pytest ./biopandas -sv` and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., `PYTHONPATH='.' pytest ./biopandas/classifier/tests/test_stacking_cv_classifier.py -sv`)
 - [ ] Checked for style issues by running `flake8 ./biopandas`
-- [ ] Added a note about the modification or contribution to the `./docs/sources/`CHANGELOG.md` file
-- [ ] Modified documentation in the appropriate location under `biopandas/docs/sources/` (optional)
-- [ ] Checked that the Travis-CI build passed at https://travis-ci.org/rasbt/biopandas
-
-
 
 
-<!--
-NOTE
-
+<!--NOTE 
 Due to the improved GitHub UI, the squashing of commits is no longer necessary.
 Please DO NOT SQUASH commits since they help with keeping track of the changes during the discussion).
-
-For more information and instructions, please see http://rasbt.github.io/biopandas/contributing/
 -->

.gitignore

@@ -1,3 +1,4 @@
+site
 docs/py-docstring-parser/
 docs/site/
 docs/sources/api_modules/

README.md

@@ -1,4 +1,4 @@
-![Logo](./docs/sources/img/logos/logo.png)
+![Logo](./docs/img/logos/logo.png)
 
 **Working with molecular structures in pandas DataFrames**
 
@@ -34,7 +34,7 @@ So, why don't we take pandas to the structural biology world? Working with molec
 
 ## Examples
 
-![3eiy](./docs/sources/img/index/3eiy.png)
+![3eiy](./docs/img/index/3eiy.png)
 
 ```python
 # Initialize a new PandasPdb object
@@ -44,13 +44,13 @@ So, why don't we take pandas to the structural biology world? Working with molec
 >>> ppdb.df['ATOM'].head()
 ```
 
-![3eiy head](./docs/sources/img/index/3eiy_head.png)
+![3eiy head](./docs/img/index/3eiy_head.png)
 
 <br><br>
 <br><br>
 
 
-![3eiy head](./docs/sources/img/index/ligand_rmsd.png)
+![3eiy head](./docs/img/index/ligand_rmsd.png)
 
 ```python
 # Load structures from your drive and compute the

biopandas/__init__.py

@@ -24,5 +24,5 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.2.5'
+__version__ = '0.2.6'
 __author__ = "Sebastian Raschka <[email protected]>"

biopandas/pdb/pandas_pdb.py

@@ -262,7 +262,7 @@ def _read_pdb(path):
  def _fetch_pdb(pdb_code):
  """Load PDB file from rcsb.org."""
  txt = None
- url = 'http://www.rcsb.org/pdb/files/%s.pdb' % pdb_code.lower()
+ url = 'https://files.rcsb.org/download/%s.pdb' % pdb_code.lower()
  try:
  response = urlopen(url)
  txt = response.read()

biopandas/pdb/tests/test_read_pdb.py

@@ -71,7 +71,7 @@ def test_fetch_pdb():
  txt[:100] == three_eiy[:100]
  ppdb.fetch_pdb('3eiy')
  assert ppdb.pdb_text == txt
- assert ppdb.pdb_path == 'http://www.rcsb.org/pdb/files/3eiy.pdb'
+ assert ppdb.pdb_path == 'https://files.rcsb.org/download/3eiy.pdb'
 
 
 def test__read_pdb_gz():