updates to documentation, dependencies, removed Travis config

Author: iskandr

.travis.yml

@@ -1,29 +1,28 @@
-Contributing to PyEnsembl
-==========================
+# Contributing to PyEnsembl
 
 [PyEnsembl](http://www.github.com/hammerlab/pyensembl) is open source software and
 we welcome your contributions. This document should help you get started
 contributing to PyEnsembl.
 
-Filing Issues
--------------
+## Filing Issues
+
 If you find any bugs or problems while using PyEnsembl or have any feature requests, please feel free to file an issue against the project. When doing so, please follow the guidelines below:
 
 To report any bugs, issues, or feature requests, please [open an issue](https://github.com/hammerlab/pyensembl/issues)
 Please check the [current open issues](https://github.com/hammerlab/pyensembl/issues) to see if the request already exists
 If you are filing a bug report, please describe the version of PyEnsembl and Python you are using. If your problem involves a particular gene, transcript, or genomic locus, please include that information (e.g. "Missing transcript sequence for BRCA1-002 for Ensembl release 74").
 
-Coding Guidelines
------------------
-* PyEnsembl is written in Python and adheres to the [PEP8](https://www.python.org/dev/peps/pep-0008/)
-style guidelines.
-* Contributions should come in the form of GitHub pull requests.
-* New features should start with a GitHub issue explaining their scope and rationale.
-* If the work is based on an existing issue, please reference the issue in the PR.
-* All new code should be accompanied by comprehensive unit tests.
-* If the PR fixes or implements an issue, please state "Closes #XYZ" or "Fixes #XYZ", where XYZ is the issue number.
-* Please ensure that your code works under both Python 2.7.x and Python >= 3.5.
-
-Licensing
----------
-PyEnsembl is licensed under the Apache 2.0 license. Your code is assumed to be as well.
+## Coding Guidelines
+
+- PyEnsembl is written in Python and adheres to the [PEP8](https://www.python.org/dev/peps/pep-0008/)
+  style guidelines.
+- Contributions should come in the form of GitHub pull requests.
+- New features should start with a GitHub issue explaining their scope and rationale.
+- If the work is based on an existing issue, please reference the issue in the PR.
+- All new code should be accompanied by comprehensive unit tests.
+- If the PR fixes or implements an issue, please state "Closes #XYZ" or "Fixes #XYZ", where XYZ is the issue number.
+- Please ensure that your code works under Python >= 3.7.
+
+## Licensing
+
+PyEnsembl is licensed under the Apache 2.0 license. Your code is assumed to be as well.

CONTRIBUTING.md

@@ -1,17 +1,20 @@
+<!--
 <a href="https://app.travis-ci.com/github/openvax/pyensembl">
     <img src="https://app.travis-ci.com/openvax/pyensembl.svg?branch=master" alt="Build Status" />
 </a>
+-->
+<!--
 <a href="https://coveralls.io/github/openvax/pyensembl?branch=master">
     <img src="https://coveralls.io/repos/openvax/pyensembl/badge.svg?branch=master&service=github" alt="Coverage Status" />
 </a>
+-->
 <a href="https://pypi.python.org/pypi/pyensembl/">
     <img src="https://img.shields.io/pypi/v/pyensembl.svg?maxAge=1000" alt="PyPI" />
 </a>
 
+# PyEnsembl
 
-PyEnsembl
-=======
-PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files. 
+PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files.
 
 # Example Usage
 
@@ -52,6 +55,7 @@ Alternatively, you can create the `EnsemblRelease` object from inside a Python
 process and call `ensembl_object.download()` followed by `ensembl_object.index()`.
 
 ## Cache Location
+
 By default, PyEnsembl uses the platform-specific `Cache` folder
 and caches the files into the `pyensembl` sub-directory.
 You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`
@@ -70,7 +74,7 @@ os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
 # ... PyEnsembl API usage
 ```
 
-# Usage tips 
+# Usage tips
 
 ## List installed genomes
 
@@ -142,8 +146,8 @@ gene_names = data.gene_names_at_locus(contig=6, position=29945884)
 # API
 
 The `EnsemblRelease` object has methods to let you access all possible
-combinations of the annotation features *gene\_name*, *gene\_id*,
-*transcript\_name*, *transcript\_id*, *exon\_id* as well as the location of
+combinations of the annotation features _gene_name_, _gene_id_,
+_transcript_name_, _transcript_id_, _exon_id_ as well as the location of
 these genomic elements (contig, start position, end position, strand).
 
 ## Genes

README.md

@@ -2,7 +2,6 @@
 
 This document explains what do once your [Pull Request](https://www.atlassian.com/git/tutorials/making-a-pull-request/) has been reviewed and all final changes applied. Now you're ready merge your branch into master and release it to the world:
 
-0. Make sure that you have `pandoc` and `pypandoc` installed: this is needed for readme markdown on PyPI. (See [here](http://pandoc.org/installing.html) and [here](https://pypi.python.org/pypi/pypandoc), respectively, for instructions.)
-1. Bump the [version](http://semver.org/) in `__init__.py`, as part of the PR you want to release.
+1. Bump the [version](http://semver.org/) in `version.py`, as part of the PR you want to release.
 2. Merge your branch into master.
-3. Travis has been configured to auto-deploy to PyPI, as long as the tests succeed and the library version is newer than any released. 
+3. Run `deploy.sh`

RELEASING.md

@@ -206,6 +206,8 @@ def create(self, overwrite=False):
         df = self._load_gtf_as_dataframe(
             usecols=self.restrict_gtf_columns, features=self.restrict_gtf_features
         )
+        if hasattr(df, "to_pandas"):
+            df = df.to_pandas()
         all_index_groups = self._all_possible_indices(df.columns)
 
         if self.restrict_gtf_features:
@@ -221,7 +223,7 @@ def create(self, overwrite=False):
         primary_keys = {}
 
         for feature in feature_names:
-            df_subset = df[df.feature == feature]
+            df_subset = df[df["feature"] == feature]
             if len(df_subset) == 0:
                 continue
             dataframes[feature] = df_subset

pyensembl/database.py

@@ -1 +1 @@
-__version__ = "2.3.4"
+__version__ = "2.3.5"

pyensembl/version.py

@@ -1,7 +1,7 @@
 typechecks>=0.0.2,<1.0.0
-datacache>=1.1.4,<2.0.0
+datacache>=1.4.0,<2.0.0
 memoized-property>=1.0.2
-tinytimer
-gtfparse>=2.2.1,<3.0.0
-serializable
-pylint>=1.4.4
+tinytimer>=0.0.0,<1.0.0
+gtfparse>=2.4.0,<3.0.0
+serializable>=0.2.1,<1.0.0
+pylint>=1.4.4,<2.0.0

requirements.txt

@@ -47,7 +47,7 @@
     setup(
         name=package_name,
         version=version,
-        description="Python interface to ensembl reference genome metadata",
+        description="Python interface to Ensembl reference genome metadata",
         author="Alex Rubinsteyn",
         author_email="[email protected]",
         url=github_url,
@@ -56,7 +56,7 @@
             "console_scripts": ["pyensembl = %s.shell:run" % package_name],
         },
         classifiers=[
-            "Development Status :: 3 - Alpha",
+            "Development Status :: 4 - Beta",
             "Environment :: Console",
             "Operating System :: OS Independent",
             "Intended Audience :: Science/Research",