automatic import of python-palos

3 files changed, 391 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..4b8b1d2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/Palos-0.1.37.tar.gz
diff --git a/python-palos.spec b/python-palos.spec
new file mode 100644
index 0000000..795dc42
--- /dev/null
+++ b/python-palos.spec
@@ -0,0 +1,389 @@
+%global _empty_manifest_terminate_build 0
+Name:		python-Palos
+Version:	0.1.37
+Release:	1
+Summary:	Misc Python modules developed and used by the yfish group
+License:	Apache2
+URL:		https://github.com/polyactis/pymodule
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/cd/61/3c79279426d3410301521c21589924960d1868d88d0ba3bb9227dd88cf49/Palos-0.1.37.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-h5py
+Requires:	python3-matplotlib
+Requires:	python3-numpy
+Requires:	python3-scipy
+Requires:	python3-sqlalchemy
+Requires:	python3-statsmodels
+Requires:	python3-tables
+Requires:	python3-future
+Requires:	python3-future-fstrings
+Requires:	python3-biopython
+Requires:	python3-pegaflow
+
+%description
+- [1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).](#1-a-repo-that-contains-miscellaneous-pythonc-modulesprograms-a-standalone-python-module-palos-by-the-yfish-group-can-be-installed-by-pip)
+- [2 Prerequisites to run Python programs in Pymodule](#2-prerequisites-to-run-python-programs-in-pymodule)
+  - [2.1 PyPi package: Palos](#21-pypi-package-palos)
+  - [2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3](#211-package-future-fstrings-ensures-compatibility-between-python2-and-python3)
+  - [2.1.2 Build and upload the palos package to PyPi](#212-build-and-upload-the-palos-package-to-pypi)
+  - [2.2 Optional prerequisites](#22-optional-prerequisites)
+  - [2.3 Optional C++ libraries](#23-optional-c-libraries)
+- [3 Example on how to run some pymodule programs](#3-example-on-how-to-run-some-pymodule-programs)
+
+Yu S. Huang, polyactis@gmail.com
+
+# 1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).
+
+This repository is a mix of a python module 'palos' and other standalone programs developed and used by the yfish group, http://www.yfish.org/.
+
+It contains code related to bioinformatics projects focusing on next-generation sequencing data, population genetics, genome-wide association studies, pedigree genetics, etc.
+
+[palos/](palos/) contains the source code of the [https://pypi.org/project/palos](https://pypi.org/project/palos) module. 
+
+[palos/algorithm/](palos/algorithm/) contains pure algorithms, not specific to Bioinformatics.
+
+
+[GADA/](GADA/) contains a faster algorithm than the original GADA (2008/2009) by using a Red-Black tree. Now in an independent repo https://github.com/polyactis/eGADA.
+
+[ngs/](ngs/) contains programs analyzing next-generation sequencing data.
+
+# 2 Prerequisites to run Python programs in Pymodule
+Most programs in pymodule are dependent on the `palos` module, which is in [palos/](palos/). Installation of `palos` will trigger installation of other dependencies.
+
+## 2.1 PyPi package: Palos
+Palos supports Python3 primarily, but is ported to Python2 via https://github.com/asottile/future-fstrings because some pymodule programs are Python2-only.
+
+Install/Upgrade the Python3 version of Palos
+```sh
+pip3 install --upgrade palos
+```
+
+
+Install/Upgrade the Python2 version of Palos
+```sh
+# to run some Python2 pymodule programs
+pip install --upgrade palos
+```
+
+## 2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3
+
+Package future-fstrings allows the use of f-string in Python2.
+```python
+# -*- coding: future_fstrings -*-
+thing = 'world'
+print(f'hello {thing}')
+```
+
+## 2.1.2 Build and upload the palos package to PyPi
+
+```bash
+# Build the package.
+# sdist and bdist_wheel are both commands of setup.py, not package names.
+python3 setup.py sdist bdist_wheel
+
+# (Delete old ones beforehand) and Upload the compiled package file.
+# Enter your PyPi username (__token__) and password (!= the pypi.org account password).
+twine upload dist/*
+
+```
+
+## 2.2 Optional prerequisites
+
+The following pakcages are optional, only needed for some functions.
+
+1. mysqldb
+2. biopython
+3. pegaflow https://pypi.org/project/Pegaflow/
+4. psycopg2 http://initd.org/psycopg/
+5. matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/
+6. python imaging library http://www.pythonware.com/products/pil/
+7. python-scientific http://www.scipy.org/
+8. biopython
+9. python-rpy2
+10. networkx https://networkx.lanl.gov/wiki
+11. hcluster
+12. python-h5py
+13. python-tables
+
+## 2.3 Optional C++ libraries
+
+Required if you plan to compile all binaries in pymodule by typeing 'make all'.
+
+apt-get install libhdf5-dev libhdf5-serial-dev libhdf5-cpp-100 hdf5-tools \
+       libarmadillo-dev libboost-program-options-dev libboost-iostreams-dev \
+       libboost-python-dev python-dev
+
+
+
+# 3 Example on how to run some pymodule programs
+
+```sh
+./ngs/DownsampleWorkflow.py  -h
+```
+
+
+
+
+
+%package -n python3-Palos
+Summary:	Misc Python modules developed and used by the yfish group
+Provides:	python-Palos
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-Palos
+- [1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).](#1-a-repo-that-contains-miscellaneous-pythonc-modulesprograms-a-standalone-python-module-palos-by-the-yfish-group-can-be-installed-by-pip)
+- [2 Prerequisites to run Python programs in Pymodule](#2-prerequisites-to-run-python-programs-in-pymodule)
+  - [2.1 PyPi package: Palos](#21-pypi-package-palos)
+  - [2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3](#211-package-future-fstrings-ensures-compatibility-between-python2-and-python3)
+  - [2.1.2 Build and upload the palos package to PyPi](#212-build-and-upload-the-palos-package-to-pypi)
+  - [2.2 Optional prerequisites](#22-optional-prerequisites)
+  - [2.3 Optional C++ libraries](#23-optional-c-libraries)
+- [3 Example on how to run some pymodule programs](#3-example-on-how-to-run-some-pymodule-programs)
+
+Yu S. Huang, polyactis@gmail.com
+
+# 1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).
+
+This repository is a mix of a python module 'palos' and other standalone programs developed and used by the yfish group, http://www.yfish.org/.
+
+It contains code related to bioinformatics projects focusing on next-generation sequencing data, population genetics, genome-wide association studies, pedigree genetics, etc.
+
+[palos/](palos/) contains the source code of the [https://pypi.org/project/palos](https://pypi.org/project/palos) module. 
+
+[palos/algorithm/](palos/algorithm/) contains pure algorithms, not specific to Bioinformatics.
+
+
+[GADA/](GADA/) contains a faster algorithm than the original GADA (2008/2009) by using a Red-Black tree. Now in an independent repo https://github.com/polyactis/eGADA.
+
+[ngs/](ngs/) contains programs analyzing next-generation sequencing data.
+
+# 2 Prerequisites to run Python programs in Pymodule
+Most programs in pymodule are dependent on the `palos` module, which is in [palos/](palos/). Installation of `palos` will trigger installation of other dependencies.
+
+## 2.1 PyPi package: Palos
+Palos supports Python3 primarily, but is ported to Python2 via https://github.com/asottile/future-fstrings because some pymodule programs are Python2-only.
+
+Install/Upgrade the Python3 version of Palos
+```sh
+pip3 install --upgrade palos
+```
+
+
+Install/Upgrade the Python2 version of Palos
+```sh
+# to run some Python2 pymodule programs
+pip install --upgrade palos
+```
+
+## 2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3
+
+Package future-fstrings allows the use of f-string in Python2.
+```python
+# -*- coding: future_fstrings -*-
+thing = 'world'
+print(f'hello {thing}')
+```
+
+## 2.1.2 Build and upload the palos package to PyPi
+
+```bash
+# Build the package.
+# sdist and bdist_wheel are both commands of setup.py, not package names.
+python3 setup.py sdist bdist_wheel
+
+# (Delete old ones beforehand) and Upload the compiled package file.
+# Enter your PyPi username (__token__) and password (!= the pypi.org account password).
+twine upload dist/*
+
+```
+
+## 2.2 Optional prerequisites
+
+The following pakcages are optional, only needed for some functions.
+
+1. mysqldb
+2. biopython
+3. pegaflow https://pypi.org/project/Pegaflow/
+4. psycopg2 http://initd.org/psycopg/
+5. matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/
+6. python imaging library http://www.pythonware.com/products/pil/
+7. python-scientific http://www.scipy.org/
+8. biopython
+9. python-rpy2
+10. networkx https://networkx.lanl.gov/wiki
+11. hcluster
+12. python-h5py
+13. python-tables
+
+## 2.3 Optional C++ libraries
+
+Required if you plan to compile all binaries in pymodule by typeing 'make all'.
+
+apt-get install libhdf5-dev libhdf5-serial-dev libhdf5-cpp-100 hdf5-tools \
+       libarmadillo-dev libboost-program-options-dev libboost-iostreams-dev \
+       libboost-python-dev python-dev
+
+
+
+# 3 Example on how to run some pymodule programs
+
+```sh
+./ngs/DownsampleWorkflow.py  -h
+```
+
+
+
+
+
+%package help
+Summary:	Development documents and examples for Palos
+Provides:	python3-Palos-doc
+%description help
+- [1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).](#1-a-repo-that-contains-miscellaneous-pythonc-modulesprograms-a-standalone-python-module-palos-by-the-yfish-group-can-be-installed-by-pip)
+- [2 Prerequisites to run Python programs in Pymodule](#2-prerequisites-to-run-python-programs-in-pymodule)
+  - [2.1 PyPi package: Palos](#21-pypi-package-palos)
+  - [2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3](#211-package-future-fstrings-ensures-compatibility-between-python2-and-python3)
+  - [2.1.2 Build and upload the palos package to PyPi](#212-build-and-upload-the-palos-package-to-pypi)
+  - [2.2 Optional prerequisites](#22-optional-prerequisites)
+  - [2.3 Optional C++ libraries](#23-optional-c-libraries)
+- [3 Example on how to run some pymodule programs](#3-example-on-how-to-run-some-pymodule-programs)
+
+Yu S. Huang, polyactis@gmail.com
+
+# 1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).
+
+This repository is a mix of a python module 'palos' and other standalone programs developed and used by the yfish group, http://www.yfish.org/.
+
+It contains code related to bioinformatics projects focusing on next-generation sequencing data, population genetics, genome-wide association studies, pedigree genetics, etc.
+
+[palos/](palos/) contains the source code of the [https://pypi.org/project/palos](https://pypi.org/project/palos) module. 
+
+[palos/algorithm/](palos/algorithm/) contains pure algorithms, not specific to Bioinformatics.
+
+
+[GADA/](GADA/) contains a faster algorithm than the original GADA (2008/2009) by using a Red-Black tree. Now in an independent repo https://github.com/polyactis/eGADA.
+
+[ngs/](ngs/) contains programs analyzing next-generation sequencing data.
+
+# 2 Prerequisites to run Python programs in Pymodule
+Most programs in pymodule are dependent on the `palos` module, which is in [palos/](palos/). Installation of `palos` will trigger installation of other dependencies.
+
+## 2.1 PyPi package: Palos
+Palos supports Python3 primarily, but is ported to Python2 via https://github.com/asottile/future-fstrings because some pymodule programs are Python2-only.
+
+Install/Upgrade the Python3 version of Palos
+```sh
+pip3 install --upgrade palos
+```
+
+
+Install/Upgrade the Python2 version of Palos
+```sh
+# to run some Python2 pymodule programs
+pip install --upgrade palos
+```
+
+## 2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3
+
+Package future-fstrings allows the use of f-string in Python2.
+```python
+# -*- coding: future_fstrings -*-
+thing = 'world'
+print(f'hello {thing}')
+```
+
+## 2.1.2 Build and upload the palos package to PyPi
+
+```bash
+# Build the package.
+# sdist and bdist_wheel are both commands of setup.py, not package names.
+python3 setup.py sdist bdist_wheel
+
+# (Delete old ones beforehand) and Upload the compiled package file.
+# Enter your PyPi username (__token__) and password (!= the pypi.org account password).
+twine upload dist/*
+
+```
+
+## 2.2 Optional prerequisites
+
+The following pakcages are optional, only needed for some functions.
+
+1. mysqldb
+2. biopython
+3. pegaflow https://pypi.org/project/Pegaflow/
+4. psycopg2 http://initd.org/psycopg/
+5. matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/
+6. python imaging library http://www.pythonware.com/products/pil/
+7. python-scientific http://www.scipy.org/
+8. biopython
+9. python-rpy2
+10. networkx https://networkx.lanl.gov/wiki
+11. hcluster
+12. python-h5py
+13. python-tables
+
+## 2.3 Optional C++ libraries
+
+Required if you plan to compile all binaries in pymodule by typeing 'make all'.
+
+apt-get install libhdf5-dev libhdf5-serial-dev libhdf5-cpp-100 hdf5-tools \
+       libarmadillo-dev libboost-program-options-dev libboost-iostreams-dev \
+       libboost-python-dev python-dev
+
+
+
+# 3 Example on how to run some pymodule programs
+
+```sh
+./ngs/DownsampleWorkflow.py  -h
+```
+
+
+
+
+
+%prep
+%autosetup -n Palos-0.1.37
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-Palos -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.37-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..ddb89d1
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+9a38ebcd21b35c22494a8dfacad7edd6  Palos-0.1.37.tar.gz