wip/py-efmlrs: import py37-efmlrs-2.1.3

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: wip/py-efmlrs: import py37-efmlrs-2.1.3
From: K.I.A.Derouiche <kamel.derouiche%gmail.com@localhost>
Date: Mon, 14 Sep 2020 00:44:00 +0000
Module Name:	pkgsrc-wip
Committed By:	K.I.A.Derouiche <kamel.derouiche%gmail.com@localhost>
Pushed By:	jihbed
Date:		Mon Sep 14 01:44:00 2020 +0100
Changeset:	08b75e498fd5e595ddcfd2c72ec89cb5c8dc76ec

Added Files:
	py-efmlrs/DESCR
	py-efmlrs/Makefile
	py-efmlrs/PLIST
	py-efmlrs/distinfo

Log Message:
wip/py-efmlrs: import py37-efmlrs-2.1.3

EFMlrs EFMlrs is a Python package combined with a designated workflow that
makes it easy for users to calculate elementary flux modes (EFMs) using a
new approach in metabolic modelling - the [mplrs algorithm](http://
cgm.cs.mcgill.ca/~avis/C/lrs.html). Besides this new approach also [efmtool]
(https://csb.ethz.ch/tools/software/efmtool.html) is supported, as it uses
the most common and established algorithm for calculating EFMs - the double
description method.

The mplrs algorithm can make use of up to two thousand threads in parallel
so that for the first time EFMs can be calculated for models that are too
big to be calculated using tools e.g. efmtool that are based on the double
description method. Furthermore the EFMlrs package provides a method that
makes it possible to integrate reaction bounds from the sbml files, so that
subsets of EFMs can be calculated. This feature is compatible with both
algorithms, the mplrs algorithm and the efmtool. EFMlrs can be used as a
stand alone console python program but is flexible enough to be integrated
in already established workflows

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=08b75e498fd5e595ddcfd2c72ec89cb5c8dc76ec

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-efmlrs/DESCR    | 17 ++++++++++++
 py-efmlrs/Makefile | 19 +++++++++++++
 py-efmlrs/PLIST    | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 py-efmlrs/distinfo |  6 ++++
 4 files changed, 123 insertions(+)

diffs:
diff --git a/py-efmlrs/DESCR b/py-efmlrs/DESCR
new file mode 100644
index 0000000000..c2d54e2e59
--- /dev/null
+++ b/py-efmlrs/DESCR
@@ -0,0 +1,17 @@
+EFMlrs EFMlrs is a Python package combined with a designated workflow that
+makes it easy for users to calculate elementary flux modes (EFMs) using a
+new approach in metabolic modelling - the [mplrs algorithm](http://
+cgm.cs.mcgill.ca/~avis/C/lrs.html). Besides this new approach also [efmtool]
+(https://csb.ethz.ch/tools/software/efmtool.html) is supported, as it uses
+the most common and established algorithm for calculating EFMs - the double
+description method.
+
+The mplrs algorithm can make use of up to two thousand threads in parallel
+so that for the first time EFMs can be calculated for models that are too
+big to be calculated using tools e.g. efmtool that are based on the double
+description method. Furthermore the EFMlrs package provides a method that
+makes it possible to integrate reaction bounds from the sbml files, so that
+subsets of EFMs can be calculated. This feature is compatible with both
+algorithms, the mplrs algorithm and the efmtool. EFMlrs can be used as a
+stand alone console python program but is flexible enough to be integrated
+in already established workflows
diff --git a/py-efmlrs/Makefile b/py-efmlrs/Makefile
new file mode 100644
index 0000000000..220d8d5e2d
--- /dev/null
+++ b/py-efmlrs/Makefile
@@ -0,0 +1,19 @@
+# $NetBSD$
+
+DISTNAME=	efmlrs-2.1.3
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=	math python
+MASTER_SITES=	https://files.pythonhosted.org/packages/ee/f0/ab1af72bb71db7fd769a42b0bf4ffc34ebf1d8a3d1baf80abd240bc290a5/
+
+MAINTAINER=	jihbed.research%gmail.com@localhost
+HOMEPAGE=	https://github.com/BeeAnka/EFMlrs
+COMMENT=	Extracts EFMs from result file of mplrs and decompresses EFMs
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	${PYPKGPREFIX}-pandas>=0.25.3:../../math/py-pandas
+DEPENDS+=	${PYPKGPREFIX}-sympy>=1.5.1:../../math/py-sympy
+
+BUILDLINK_API_DEPENDS.py-numpy+=	${PYPKGPREFIX}-numpy>=1.0
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-efmlrs/PLIST b/py-efmlrs/PLIST
new file mode 100644
index 0000000000..379bbdd45e
--- /dev/null
+++ b/py-efmlrs/PLIST
@@ -0,0 +1,81 @@
+@comment $NetBSD$
+bin/efmlrs_post
+bin/efmlrs_pre
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/efmlrs/__init__.py
+${PYSITELIB}/efmlrs/__init__.pyc
+${PYSITELIB}/efmlrs/__init__.pyo
+${PYSITELIB}/efmlrs/_version.py
+${PYSITELIB}/efmlrs/_version.pyc
+${PYSITELIB}/efmlrs/_version.pyo
+${PYSITELIB}/efmlrs/post.py
+${PYSITELIB}/efmlrs/post.pyc
+${PYSITELIB}/efmlrs/post.pyo
+${PYSITELIB}/efmlrs/postprocessing/__init__.py
+${PYSITELIB}/efmlrs/postprocessing/__init__.pyc
+${PYSITELIB}/efmlrs/postprocessing/__init__.pyo
+${PYSITELIB}/efmlrs/postprocessing/decompressing.py
+${PYSITELIB}/efmlrs/postprocessing/decompressing.pyc
+${PYSITELIB}/efmlrs/postprocessing/decompressing.pyo
+${PYSITELIB}/efmlrs/postprocessing/decompressions/__init__.py
+${PYSITELIB}/efmlrs/postprocessing/decompressions/__init__.pyc
+${PYSITELIB}/efmlrs/postprocessing/decompressions/__init__.pyo
+${PYSITELIB}/efmlrs/postprocessing/decompressions/deadend.py
+${PYSITELIB}/efmlrs/postprocessing/decompressions/deadend.pyc
+${PYSITELIB}/efmlrs/postprocessing/decompressions/deadend.pyo
+${PYSITELIB}/efmlrs/postprocessing/decompressions/null_space.py
+${PYSITELIB}/efmlrs/postprocessing/decompressions/null_space.pyc
+${PYSITELIB}/efmlrs/postprocessing/decompressions/null_space.pyo
+${PYSITELIB}/efmlrs/postprocessing/decompressions/one2many.py
+${PYSITELIB}/efmlrs/postprocessing/decompressions/one2many.pyc
+${PYSITELIB}/efmlrs/postprocessing/decompressions/one2many.pyo
+${PYSITELIB}/efmlrs/postprocessing/get_data.py
+${PYSITELIB}/efmlrs/postprocessing/get_data.pyc
+${PYSITELIB}/efmlrs/postprocessing/get_data.pyo
+${PYSITELIB}/efmlrs/pre.py
+${PYSITELIB}/efmlrs/pre.pyc
+${PYSITELIB}/efmlrs/pre.pyo
+${PYSITELIB}/efmlrs/preprocessing/__init__.py
+${PYSITELIB}/efmlrs/preprocessing/__init__.pyc
+${PYSITELIB}/efmlrs/preprocessing/__init__.pyo
+${PYSITELIB}/efmlrs/preprocessing/boundaries.py
+${PYSITELIB}/efmlrs/preprocessing/boundaries.pyc
+${PYSITELIB}/efmlrs/preprocessing/boundaries.pyo
+${PYSITELIB}/efmlrs/preprocessing/compressions/__init__.py
+${PYSITELIB}/efmlrs/preprocessing/compressions/__init__.pyc
+${PYSITELIB}/efmlrs/preprocessing/compressions/__init__.pyo
+${PYSITELIB}/efmlrs/preprocessing/compressions/deadend.py
+${PYSITELIB}/efmlrs/preprocessing/compressions/deadend.pyc
+${PYSITELIB}/efmlrs/preprocessing/compressions/deadend.pyo
+${PYSITELIB}/efmlrs/preprocessing/compressions/echelon.py
+${PYSITELIB}/efmlrs/preprocessing/compressions/echelon.pyc
+${PYSITELIB}/efmlrs/preprocessing/compressions/echelon.pyo
+${PYSITELIB}/efmlrs/preprocessing/compressions/null_space.py
+${PYSITELIB}/efmlrs/preprocessing/compressions/null_space.pyc
+${PYSITELIB}/efmlrs/preprocessing/compressions/null_space.pyo
+${PYSITELIB}/efmlrs/preprocessing/compressions/one2many.py
+${PYSITELIB}/efmlrs/preprocessing/compressions/one2many.pyc
+${PYSITELIB}/efmlrs/preprocessing/compressions/one2many.pyo
+${PYSITELIB}/efmlrs/preprocessing/get_data.py
+${PYSITELIB}/efmlrs/preprocessing/get_data.pyc
+${PYSITELIB}/efmlrs/preprocessing/get_data.pyo
+${PYSITELIB}/efmlrs/preprocessing/mplrs_output.py
+${PYSITELIB}/efmlrs/preprocessing/mplrs_output.pyc
+${PYSITELIB}/efmlrs/preprocessing/mplrs_output.pyo
+${PYSITELIB}/efmlrs/util/__init__.py
+${PYSITELIB}/efmlrs/util/__init__.pyc
+${PYSITELIB}/efmlrs/util/__init__.pyo
+${PYSITELIB}/efmlrs/util/convert_matrix.py
+${PYSITELIB}/efmlrs/util/convert_matrix.pyc
+${PYSITELIB}/efmlrs/util/convert_matrix.pyo
+${PYSITELIB}/efmlrs/util/data.py
+${PYSITELIB}/efmlrs/util/data.pyc
+${PYSITELIB}/efmlrs/util/data.pyo
+${PYSITELIB}/efmlrs/util/log.py
+${PYSITELIB}/efmlrs/util/log.pyc
+${PYSITELIB}/efmlrs/util/log.pyo
diff --git a/py-efmlrs/distinfo b/py-efmlrs/distinfo
new file mode 100644
index 0000000000..e30f2fbe96
--- /dev/null
+++ b/py-efmlrs/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (efmlrs-2.1.3.tar.gz) = d4f3fb10815e9d8ea3df3257068e8cb2e3f1ffca
+RMD160 (efmlrs-2.1.3.tar.gz) = 40c0f5d55f5568a6758c7c7085e166cf6f85954d
+SHA512 (efmlrs-2.1.3.tar.gz) = 0a7c512fa1016aa99f31efeb2ccc0bdc89e827875bba8a9bb4746632edffeb58e2e8cac1de6d041fc51ff7c04107c0814e6aae4774c431d73af62c6137db7462
+Size (efmlrs-2.1.3.tar.gz) = 1827401 bytes
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