Develop (#147)

* gzip sanitized gtfs (#127)

* more stabile testing(?) (#128)

* added rm -rf function (#126)

* added rm -rf function to fix clean

* updated code for rm_rf

* bucket changes (#129)

* update readme (#132)

* update readme

* black. extended genomepy search (was an issue to black anyway)

* fix (#133)

* argparse action to parse genome from command line option

* use genomes_dir argument

* increased maximum complexity to 10 (#137)

* remove 'alt' regions by default (#136)

* remove 'alt' regions by default

* Update CHANGELOG.md

* increase rerun delay (1 -> 5 sec)

* increase rerun delay (1 -> 10 sec)

* updated CHANGELOG.md

* Update version

* fix CHANGELOG.md

* Update CHANGELOG.md

* Progress (#141)

* tqdm progress bar for downloads & bgzipping, spinner for indexing

* improve mkdir_p and rm_rf functionality

* log removed alt-regions (#140)

* Fix 142 (#143)

* replace tempfile.TemporaryDirectory with mkdtemp and rm_rf

* updated DOI

* Update CHANGELOG.md

* update tests

* add mamba to travis

* update version & changelog

* update release checklist

Co-authored-by: Simon van Heeringen <[email protected]>

.travis.yml

@@ -22,9 +22,10 @@ before_install:
   - ./miniconda.sh -b -p $HOME/miniconda -f
   - export PATH=$HOME/miniconda/bin:$PATH
   - conda config --set always_yes yes
+  - conda install conda-forge::mamba
 
 install:
-  - conda env create -n genomepy python=$PYTHON_VERSION -f environment.yml
+  - mamba env create -n genomepy python=$PYTHON_VERSION -f environment.yml
   - source activate genomepy
   - python setup.py develop
   - python setup.py build

CHANGELOG.md

@@ -6,11 +6,19 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [0.9.2] - 2021-01-28
+
 ### Added
+- progress bars for downloading and bgzipping (the slow stuff)
+- spinner to indexing plugins (the slowest stuff)
 
 ### Changed
+- removed dependency of psutils
+- added dependency of tqdm
 
 ### Fixed
+- an oopsie in the regex filter functions slowing down `install`.
+- rm_rf and mkdir_p to behave more like their namesakes.
 
 ## [0.9.1] - 2020-10-26
 
@@ -269,6 +277,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Added `-r` and `--match/--no-match` option to select sequences by regex.
 
 [Unreleased]: https://github.com/vanheeringen-lab/genomepy/compare/master...develop
+[0.9.2]: https://github.com/vanheeringen-lab/genomepy/compare/0.9.1...0.9.2
 [0.9.1]: https://github.com/vanheeringen-lab/genomepy/compare/0.9.0...0.9.1
 [0.9.0]: https://github.com/vanheeringen-lab/genomepy/compare/0.8.4...0.9.0
 [0.8.4]: https://github.com/vanheeringen-lab/genomepy/compare/0.8.3...0.8.4

README.md

@@ -10,7 +10,7 @@
 [![Test Coverage](https://api.codeclimate.com/v1/badges/c4476820f1d21a3e0569/test_coverage)](https://codeclimate.com/github/vanheeringen-lab/genomepy/test_coverage)
 
 [![status](http://joss.theoj.org/papers/df434a15edd00c8c2f4076668575d1cd/status.svg)](http://joss.theoj.org/papers/df434a15edd00c8c2f4076668575d1cd)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.831969.svg)](https://doi.org/10.5281/zenodo.831969)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1010458.svg)](https://doi.org/10.5281/zenodo.1010458)
 
 Easily install and use genomes in Python and elsewhere!
 

docs/release_checklist.md

@@ -3,7 +3,8 @@
 1. Create release candidate with `git flow`:
 
 ```
-$ git flow release start ${new_version} 
+new_version=0.0.0
+git flow release start ${new_version}
 ```
 
 2. Update version in `genomepy/__about__.py`
@@ -19,9 +20,13 @@ $ git flow release start ${new_version}
 
 ```
 python setup.py sdist bdist_wheel
-twine upload --repository-url https://test.pypi.org/legacy/ dist/genomepy-${version}*
 
-pip install --extra-index-url https://test.pypi.org/simple/ genomepy==${version}
+# twine must be up to date (3.3.0 works). System installed twine can interfere.
+twine upload --repository-url https://test.pypi.org/legacy/ dist/genomepy-${new_version}*
+
+# the \ is to escape the ==, so the variable ${new_version} can be called
+pip install --extra-index-url https://test.pypi.org/simple/ genomepy\==${new_version}
+
 genomepy search xenopus_tropicalis
 ```
 

environment.yml

@@ -11,9 +11,9 @@ dependencies:
   - click
   - colorama
   - norns>=0.1.5
-  - psutil
   - pyfaidx>=0.5.7
   - requests
+  - tqdm>=4.51
 
   # Bgzip
   - tabix

genomepy/__about__.py

@@ -1,3 +1,3 @@
 """Metadata"""
-__version__ = "0.9.1"
+__version__ = "0.9.2"
 __author__ = "Simon van Heeringen"

genomepy/plugins/gmap.py

@@ -1,6 +1,6 @@
 import os.path
 from shutil import move
-from tempfile import TemporaryDirectory
+from tempfile import mkdtemp
 from genomepy.plugin import Plugin
 from genomepy.utils import cmd_ok, rm_rf, run_index_cmd, gunzip_and_name, bgzip_and_name
 
@@ -22,14 +22,15 @@ def after_genome_download(self, genome, threads=1, force=False):
 
             # gmap outputs a folder named genome.name
             # its content is moved to index dir, consistent with other plugins
-            with TemporaryDirectory() as tmpdir:
-                # Create index
-                cmd = f"gmap_build -D {tmpdir} -d {genome.name} {fname}"
-                run_index_cmd("gmap", cmd)
-
-                # Move files to index_dir
-                src = os.path.join(tmpdir, genome.name)
-                move(src, index_dir)
+            tmp_dir = mkdtemp(dir=".")
+            # Create index
+            cmd = f"gmap_build -D {tmp_dir} -d {genome.name} {fname}"
+            run_index_cmd("gmap", cmd)
+
+            # Move files to index_dir
+            src = os.path.join(tmp_dir, genome.name)
+            move(src, index_dir)
+            rm_rf(tmp_dir)
 
             # re-zip genome if unzipped
             bgzip_and_name(fname, bgzip)