From c8365cce6e47bf4aa33d2611f85fe7f4e7ae9cc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20Mart=C3=AD?= <--global> Date: Tue, 22 Nov 2022 10:42:46 -0800 Subject: [PATCH 01/10] Removed the 'python setup.py develop' from build.sh as it was causing an error when trying to connect to pypi. --- build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.sh b/build.sh index c23e16ca..d1d52ab5 100644 --- a/build.sh +++ b/build.sh @@ -1,3 +1,3 @@ #!/usr/bin/env bash $PYTHON setup.py build -$PYTHON setup.py install develop --user +# $PYTHON setup.py develop --user From aa9d6af452c5a1e3f03262447759a097910330f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20Mart=C3=AD?= <--global> Date: Tue, 22 Nov 2022 11:01:21 -0800 Subject: [PATCH 02/10] Changes in conda packaging (meta.yaml). Added Jinja templates for package name and version. Use github as source. Build entry points. Use conda-forge versions of packages. Added further metadata of the package. --- meta.yaml | 38 +++++++++++++++++++++++++------------- 1 file changed, 25 insertions(+), 13 deletions(-) diff --git a/meta.yaml b/meta.yaml index 913dad63..d4a0d2fb 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,30 +1,42 @@ -# cmd: conda build . -c zadorlab -c openbabel -c conda-forge +# cmd: conda build . -c conda-forge + +{% set name = "kinbot" %} +{% set version = "v2.0.6" %} + package: - name: kinbot - version: "2.0" + name: {{ name|lower }} + version: {{ version }} source: - path: . + url: https://github.com/zadorlab/KinBot/archive/refs/tags/{{ version }}.tar.gz build: + entry_points: + - kinbot = kinbot.kb:main + - pes = kinbot.pes:main noarch: python requirements: - build: - - python {{ python }} - - numpy {{ numpy }} host: - - python + - python >=3.6 + - setuptools run: - - python {{ python }} - - numpy {{ numpy }} + - python >=3.6 + - numpy >=1.17.0 - matplotlib - networkx - - conda-forge::pyvis - - zadorlab::ase - - openbabel::openbabel + - pyvis + - openbabel + - ase about: home: https://github.com/zadorlab/KinBot license: BSD 3-clause + license_file: LICENSE + summary: Automated reaction pathway search for gas-phase molecules. + +extra: + recipe-maintainers: + - jzador + - cmartia From d09f01dd2896b08cfe0891b878cd617d9a4cc632 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20Mart=C3=AD?= <--global> Date: Tue, 22 Nov 2022 12:03:16 -0800 Subject: [PATCH 03/10] Removed 'v' from version. Changed Judit username. --- meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/meta.yaml b/meta.yaml index d4a0d2fb..24caa87e 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,7 +1,7 @@ # cmd: conda build . -c conda-forge {% set name = "kinbot" %} -{% set version = "v2.0.6" %} +{% set version = "2.0.6" %} package: name: {{ name|lower }} @@ -37,6 +37,6 @@ about: extra: recipe-maintainers: - - jzador + - juditzador - cmartia From 095e002e25d34d80613618d4c981f140a9aa34cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20Mart=C3=AD?= <--global> Date: Tue, 22 Nov 2022 14:57:35 -0800 Subject: [PATCH 04/10] Substituted build.sh for a build/script entry in meta.yaml. Added sha256 sum. Corrected url to be match version without the 'v'. Added build number. Added description doc_url and dev_url in the about section. Corrected Judit's user in conda. --- build.sh | 3 --- meta.yaml | 18 +++++++++++++++--- 2 files changed, 15 insertions(+), 6 deletions(-) delete mode 100644 build.sh diff --git a/build.sh b/build.sh deleted file mode 100644 index d1d52ab5..00000000 --- a/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/env bash -$PYTHON setup.py build -# $PYTHON setup.py develop --user diff --git a/meta.yaml b/meta.yaml index 24caa87e..a6f42985 100644 --- a/meta.yaml +++ b/meta.yaml @@ -2,19 +2,23 @@ {% set name = "kinbot" %} {% set version = "2.0.6" %} +{% set sha256 = "4fa5bf36a5aa22e5edc1080be196febc9fb6a3153b16296c5220ee601f36c8ab" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/zadorlab/KinBot/archive/refs/tags/{{ version }}.tar.gz + url: https://github.com/zadorlab/KinBot/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} build: + number: 0 + noarch: python + script: {{ PYTHON }} setup.py build entry_points: - kinbot = kinbot.kb:main - pes = kinbot.pes:main - noarch: python requirements: host: @@ -35,8 +39,16 @@ about: license_file: LICENSE summary: Automated reaction pathway search for gas-phase molecules. + description: | + KinBot is an automated gas-phase kinetics workflow code that drives + electronic structure calculations on a chemical PES and characterizes + the chemically relevant stationary points to finally create a complete + master equation formulation of the chemical kinetic system. + doc_url: https://github.com/zadorlab/KinBot/wiki + dev_url: https://github.com/zadorlab/KinBot + extra: recipe-maintainers: - - juditzador + - jzador - cmartia From 88125d1d6d97a99a98de48eb82c8bb5a47f94656 Mon Sep 17 00:00:00 2001 From: Carles Marti Date: Tue, 22 Nov 2022 16:58:59 -0800 Subject: [PATCH 05/10] Build latest version of KinBot. --- meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/meta.yaml b/meta.yaml index a6f42985..812edef5 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,15 +1,15 @@ # cmd: conda build . -c conda-forge {% set name = "kinbot" %} -{% set version = "2.0.6" %} -{% set sha256 = "4fa5bf36a5aa22e5edc1080be196febc9fb6a3153b16296c5220ee601f36c8ab" %} +{% set version = "2.0.7" %} +{% set sha256 = "08bd0adcfbe54e418ac07eeaf2c4a00b451e896dd52e9e21d0940a3152596f44" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/zadorlab/KinBot/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/zadorlab/KinBot/archive/refs/heads/master.tar.gz sha256: {{ sha256 }} build: From 2c0effe1d1dafb2c83ff691c08fdd622e7981ab4 Mon Sep 17 00:00:00 2001 From: Carles Marti Date: Tue, 22 Nov 2022 16:59:13 -0800 Subject: [PATCH 06/10] Correct name of license. --- meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/meta.yaml b/meta.yaml index 812edef5..c33ea5c0 100644 --- a/meta.yaml +++ b/meta.yaml @@ -35,7 +35,7 @@ requirements: about: home: https://github.com/zadorlab/KinBot - license: BSD 3-clause + license: BSD-3-Clause license_file: LICENSE summary: Automated reaction pathway search for gas-phase molecules. From daca39b28dff4ff58f626102d1262470fc84659f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20Mart=C3=AD?= Date: Thu, 24 Nov 2022 11:34:55 -0800 Subject: [PATCH 07/10] Corrected Judit's github username. --- meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/meta.yaml b/meta.yaml index c33ea5c0..5c28a862 100644 --- a/meta.yaml +++ b/meta.yaml @@ -49,6 +49,5 @@ about: extra: recipe-maintainers: - - jzador - - cmartia - + - juditzador + - cmartia \ No newline at end of file From 88e515732147785e0b55b4e05103fac71f67980b Mon Sep 17 00:00:00 2001 From: Carles Marti Date: Mon, 5 Dec 2022 16:48:23 -0800 Subject: [PATCH 08/10] Added first version of pyproject.toml. --- pyproject.toml | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..3c3dface --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,56 @@ +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "KinBot" +version = "2.1" +description = "Automated reaction kinetics for gas-phase species" +readme = "README.md" +requires-python = ">=3.6" +license = {file = "LICENSE"} +# keywords = [] +authors = [ + {name="Judit Zádor", email="jzador@sandia.gov"}, + {name="Ruben Vande Vijver", email="ruben.vandevijver@ugent.be"}, + {name="Carles Martí", email="cmartia@sandia.gov"}, + {name="Amanda Dewyer", email="adewyer@sandia.gov"}, +] +maintainers = [ + {name="Judit Zádor", email="jzador@sandia.gov"}, + {name="Carles Martí", email="cmartia@sandia.gov"}, +] +classifiers = [ + "Environment :: Console", + "Intended Audience :: Science/Research", + "Natural Language :: English", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Topic :: Scientific/Engineering :: Chemistry" +] +dependencies = [ + "numpy>=1.17.0", + "ase>=3.19", + "networkx", + "rmsd" +] + +[project.optional-dependencies] +plot = [ + "matplotlib", + "pyvis", + "rdkit" +] + +[project.urls] +homepage = "https://github.com/zadorlab/KinBot" +documentation = "https://github.com/zadorlab/KinBot/wiki" + +[project.scripts] +kinbot = "kinbot.kb:main" +pes = "kinbot.pes:main" \ No newline at end of file From 6aae7c3d62522a2bd13e44c56b7f22d8639de0de Mon Sep 17 00:00:00 2001 From: Carles Marti Date: Tue, 6 Dec 2022 16:33:25 -0800 Subject: [PATCH 09/10] Remove setup.py. --- setup.py | 80 -------------------------------------------------------- 1 file changed, 80 deletions(-) delete mode 100644 setup.py diff --git a/setup.py b/setup.py deleted file mode 100644 index 3c3cd90d..00000000 --- a/setup.py +++ /dev/null @@ -1,80 +0,0 @@ -""" -This file is used to install KinBot. - -Type -python setup.py build -python setup.py install -""" - -from setuptools import setup, find_packages - -setup( - name = "KinBot", - version = "2.0", - packages = find_packages(), - package_data={'tpl':[ - 'arrow.png', - 'ase_gauss_freq_well.tpl.py', - 'ase_gauss_hir.tpl.py', - 'ase_gauss_irc.tpl.py', - 'ase_gauss_opt_well.tpl.py', - 'ase_gauss_ts_end.tpl.py', - 'ase_gauss_ts_search.tpl.py', - 'ase_nwchem_freq_well.tpl.py', - 'ase_nwchem_irc.tpl.py', - 'ase_nwchem_opt_well.tpl.py', - 'ase_gauss_ring_conf.tpl.py', - 'ase_nwchem_ts_end.tpl.py', - 'ase_nwchem_ts_search.tpl.py', - 'ase_nwchem_ts_search_ase_constraints.tpl.py', - 'mess_2tst.tpl', - 'mess_atom.tpl', - 'mess_barrier.tpl', - 'mess_barrier_union.tpl', - 'mess_barrierless.tpl', - 'mess_bimol.tpl', - 'mess_core_rr.tpl', - 'mess_dummy.tpl', - 'mess_fragment.tpl', - 'mess_fragment_OH.tpl', - 'mess_pstfragment.tpl', - 'mess_header.tpl', - 'mess_hinderedrotor.tpl', - 'mess_outerrrho.tpl', - 'mess_pst.tpl', - 'mess_rrho.tpl', - 'mess_termol.tpl', - 'mess_tunneling.tpl', - 'mess_variational.tpl', - 'mess_well.tpl', - 'mess_well_union.tpl', - 'molpro.tpl', - 'pbs.tpl', - 'pbs_molpro.tpl', - 'pbs_mesmer.tpl', - 'pbs_mess.tpl', - 'pbs_mess_uq.tpl', - 'pbs_python.tpl', - 'pesviewer.inp.tpl', - 'slurm.tpl', - 'slurm_molpro.tpl', - 'slurm_mess_uq.tpl', - 'slurm_mesmer.tpl', - 'slurm_python.tpl']}, - include_package_data=True, - entry_points={'console_scripts':[ - 'kinbot = kinbot.kb:main', - 'pes = kinbot.pes:main', - ]}, - install_requires = [ - 'numpy>=1.17.0', - 'ase', - 'networkx', - 'rmsd' - ], - author="Judit Zador, Ruben Van de Vijver, Carles Marti, Amanda Dewyer", - author_email = "jzador@sandia.gov", - description = "Automated reaction kinetics for gas-phase species", - license = "BSD 3-clause", - url = "https://github.com/zadorlab/KinBot", -) From dd55603cb79434732a119017b8e41fb989ebb9c3 Mon Sep 17 00:00:00 2001 From: Carles Marti Date: Tue, 6 Dec 2022 17:48:00 -0800 Subject: [PATCH 10/10] Exclude build, dist and egg in the pyproject.toml. Use lowercase package name. --- pyproject.toml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3c3dface..24786fd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,9 +2,12 @@ requires = ["setuptools>=61.0"] build-backend = "setuptools.build_meta" +[tool.setuptools.packages.find] +exclude = ["build", "dist", "KinBot.egg-info"] + [project] -name = "KinBot" -version = "2.1" +name = "kinbot" +version = "2.1.0" description = "Automated reaction kinetics for gas-phase species" readme = "README.md" requires-python = ">=3.6"