Project: update Python to 3.9, update all dependencies#214

Merged

taimontgomery merged 17 commits intomasterfrom

issue-187

Aug 4, 2022

Commits on Jul 20, 2022

Dependencies and Python version have been upgraded for 3.9. This represents a forward jump of 2-4 years for many of these dependencies
AlexTate
committed
Update multiprocessing utilities to use fork instead of spawn. MP for py3.8 switched to spawn by default on macOS, which means that workers did not inherit global variables as expected
AlexTate
committed
Updated our parse_GFF_attribute_string() patch to reflect latest changes in HTSeq. Also removed string interning for attribute keys/values since tiny-count's design has evolved to handle these valu…
AlexTate
committed
Python now issues a warning when comparing to string literals using the "is" operator (even though the values I was comparing to are guaranteed to be interned for current and prior Python versions)
AlexTate
committed
Minor change to fix a future deprication warning from numpy
AlexTate
committed
Minor change to make the cwltool runner more useful when running the pipeline in debug mode
AlexTate
committed
The Features class now uses the improved singleton design pattern first used in the Wildcard class, for consistency
AlexTate
committed
Settling on a version compromise for r-base and nodejs (newer versions are possible on linux but not osx). Also reorganized the ordering of environment.yml.
AlexTate
committed
setup.sh has been updated to no longer install r or DESeq2 since this is now managed by conda (which also means we can skip the 20 minute wait while it compiles). Bioconductor-related variables hav…
AlexTate
committed
Removing old lockfiles for the r-included installs. Remaining lockfiles have been updated to reflect changes in environment.yml
AlexTate
committed

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Project: update Python to 3.9, update all dependencies#214

Project: update Python to 3.9, update all dependencies#214
taimontgomery merged 17 commits intomasterfrom
issue-187

Commits on Jul 20, 2022

Dependencies and Python version have been upgraded for 3.9. This represents a forward jump of 2-4 years for many of these dependencies

Update multiprocessing utilities to use fork instead of spawn. MP for py3.8 switched to spawn by default on macOS, which means that workers did not inherit global variables as expected

Updated our parse_GFF_attribute_string() patch to reflect latest changes in HTSeq. Also removed string interning for attribute keys/values since tiny-count's design has evolved to handle these valu…

Python now issues a warning when comparing to string literals using the "is" operator (even though the values I was comparing to are guaranteed to be interned for current and prior Python versions)

Minor change to fix a future deprication warning from numpy

Minor change to make the cwltool runner more useful when running the pipeline in debug mode

The Features class now uses the improved singleton design pattern first used in the Wildcard class, for consistency

Settling on a version compromise for r-base and nodejs (newer versions are possible on linux but not osx). Also reorganized the ordering of environment.yml.

setup.sh has been updated to no longer install r or DESeq2 since this is now managed by conda (which also means we can skip the 20 minute wait while it compiles). Bioconductor-related variables hav…

Removing old lockfiles for the r-included installs. Remaining lockfiles have been updated to reflect changes in environment.yml

Commits on Jul 26, 2022

Finalizing conda lock files. environment.yml has also been updated to include an environment variable which should help with installation stability on Linux. Lock files will not convey environment …

Small bugfix to address a non-numeric reduction warning

Package version corrections in setup.py

Directing stdout from `conda env config vars` to /dev/null to keep terminal output clean

Updating project description in setup.py

Commits on Jul 27, 2022

Version bugfix for the bowtie CWL wrapper. The previous method of setting the index via positional argument produces a future deprecation warning. This commit also contains a small correction to th…

The run_native runner mode was performing parallel runs regardless of user preferences for run_parallel. This has been corrected so that tinyRNA respects the run_parallel setting when run_native is…