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update setup and tox
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@fernandomeyer
fernandomeyer committed Jul 15, 2019
1 parent 8083435 commit 8ee7111
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -30,7 +30,7 @@ AMBER (Assessment of Metagenome BinnERs) is an evaluation package for the compar

## Requirements

AMBER requires Python 3.5 or above.
AMBER requires Python 3.7.

See [default.txt](requirements/default.txt) for all dependencies.

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You can use all libraries that AMBER depends on by activating tox's virtual environment with the command:

~~~BASH
source <project_directory>/.tox/py35/bin/activate
source <project_directory>/.tox/py37/bin/activate
~~~

### Update GitHub page
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8 changes: 4 additions & 4 deletions features/amber_stdout.feature
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Expand Up @@ -14,14 +14,14 @@ Feature: Run Scripts without error
| unique_common.tsv | input |
When I run the command
"""
../amber.py -g input/gsa_mapping.binning input/goofy_hypatia_2 input/naughty_carson_2 -r input/unique_common.tsv -k "circular element" -p 1 -l "CONCOCT (CAMI), MaxBin 2.0.2 (CAMI)" -o output --stdout
../amber.py -g input/gsa_mapping.binning input/goofy_hypatia_2 input/naughty_carson_2 -r input/unique_common.tsv -k "circular element" -p 1 -l "CONCOCT (CAMI), MaxBin 2.0.2 (CAMI)" -o output --stdout --silent
"""
Then the exit code should be 0
And the file "output/results.tsv" should exist
And the stdout should contain:
"""
Tool >0.5compl<0.05cont >0.5compl<0.1cont >0.7compl<0.05cont >0.7compl<0.1cont >0.9compl<0.05cont >0.9compl<0.1cont Accuracy (bp) Accuracy (seq) Adjusted Rand index (bp) Adjusted Rand index (seq) Average completeness (bp) Average completeness (seq) Average purity (bp) Average purity (seq) Completeness (bp) Completeness (seq) Misclassification rate (bp) Misclassification rate (seq) Percentage of assigned bps Percentage of assigned sequences Purity (bp) Purity (seq) Rand index (bp) Rand index (seq) Sample Std error of average completeness (bp) Std error of average completeness (seq) Std error of average purity (bp) Std error of average purity (seq) UniFrac (bp) UniFrac (seq) binning type rank
CONCOCT (CAMI) 16 18 16 17 14 15 0.663234 0.321346 0.643540 0.750520 0.516941 0.424888 0.837135 0.757099 0.935822 0.381454 0.315830 0.257567 0.969401 0.432638 0.684170 0.742433 0.971708 0.945658 CAMI_low 0.070242 0.056733 0.053293 0.063328 None None genome NA
MaxBin 2.0.2 (CAMI) 23 28 23 28 21 24 0.809257 0.319959 0.917148 0.781552 0.798593 0.702312 0.947763 0.794919 0.837613 0.368405 0.065092 0.236671 0.865600 0.419098 0.934908 0.763329 0.994690 0.951013 CAMI_low 0.058312 0.055000 0.016707 0.044926 None None genome NA
Tool >0.5compl<0.05cont >0.5compl<0.1cont >0.7compl<0.05cont >0.7compl<0.1cont >0.9compl<0.05cont >0.9compl<0.1cont Accuracy (bp) Accuracy (seq) Adjusted Rand index (bp) Adjusted Rand index (seq) Average completeness (bp) Average completeness (seq) Average purity (bp) Average purity (seq) Completeness (bp) Completeness (seq) Misclassification rate (bp) Misclassification rate (seq) Percentage of assigned bps Percentage of assigned sequences Purity (bp) Purity (seq) Rand index (bp) Rand index (seq) Sample Std error of average completeness (bp) Std error of average completeness (seq) Std error of average purity (bp) Std error of average purity (seq) UniFrac (bp) UniFrac (seq) binning type rank
CONCOCT (CAMI) 16 18 16 17 14 15 0.663234 0.321346 0.643540 0.750520 0.516941 0.424888 0.837135 0.757099 0.935822 0.381454 0.315830 0.257567 0.969401 0.432638 0.684170 0.742433 0.971708 0.945658 CAMI_low 0.070242 0.056733 0.053293 0.063328 None None genome NA
MaxBin 2.0.2 (CAMI) 23 28 23 28 21 24 0.809257 0.319959 0.917148 0.781552 0.798593 0.702312 0.947763 0.794919 0.837613 0.368405 0.065092 0.236671 0.865600 0.419098 0.934908 0.763329 0.994690 0.951013 CAMI_low 0.058312 0.055000 0.016707 0.044926 None None genome NA
"""
2 changes: 1 addition & 1 deletion setup.cfg
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@@ -1,2 +1,2 @@
[bdist_wheel]
python-tag = py35
python-tag = py37
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -22,7 +22,7 @@ def dependencies():
classifiers = [
'Natural Language :: English',
'Programming Language :: Python',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.7',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Intended Audience :: Science/Research',
'Operating System :: POSIX'
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4 changes: 2 additions & 2 deletions tox.ini
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@@ -1,12 +1,12 @@
[tox]
envlist = {py35}
envlist = {py37}
skipsdist = True

[testenv]
deps = -r{toxinidir}/requirements/development.txt
-r{toxinidir}/requirements/default.txt
basepython =
py35: python3.5
py37: python3.7
commands =
behave --stop --define TMPDIR=tmp
setenv =
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