From 73c8331e95ffbc6e8a43b74dbf378292e1c39f73 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Mon, 15 Apr 2019 04:06:55 +0800 Subject: [PATCH 1/7] chore: use docker for travis (#23) * Update .travis.yml * Update tox.ini --- .travis.yml | 21 ++++----------------- tox.ini | 2 ++ 2 files changed, 6 insertions(+), 17 deletions(-) diff --git a/.travis.yml b/.travis.yml index c551d9a..3a6e6e8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,23 +5,10 @@ sudo: false cache: directories: - $HOME/.cache/pip - +services: docker env: global: - - PYTHON_VERSION=3.7 - - PIP_DEPENDENCIES="tox-conda" - secure: "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" - -before_install: - - git clone --depth 1 https://github.com/circulosmeos/gdown.pl; - - ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1; - - tar -xzvf g16.tgz; - - export g16root=$(pwd) - - source g16/bsd/g16.profile - -install: - - git clone --depth 1 git://github.com/astropy/ci-helpers.git - - source ci-helpers/travis/setup_conda.sh - -script: - - tox +before_install: git clone --depth 1 https://github.com/circulosmeos/gdown.pl && ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1 && tar -xzvf g16.tgz; +install: docker pull continuumio/miniconda3 +script: docker run -i -t -v $(pwd):/project -v ~/.cache/pip:/root/.cache/pip --env-file <(env | grep 'TRAVIS\|CI') continuumio/miniconda3 /bin/bash -c "chown -R root /root/.cache && pip install tox-conda && cd /project && export g16root=/project && source g16/bsd/g16.profile && tox -e py37" diff --git a/tox.ini b/tox.ini index c2b380b..5016038 100644 --- a/tox.ini +++ b/tox.ini @@ -10,6 +10,8 @@ deps = codacy-coverage conda_deps= openbabel + c-compiler + cxx-compiler conda_channels= conda-forge commands = From 73d31c9161361573f00093b310c58ea3f3e2cfce Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sat, 4 May 2019 21:33:48 +0800 Subject: [PATCH 2/7] chore: use docker njzjz/tox (#24) --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 3a6e6e8..2f18a87 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,5 +10,5 @@ env: global: - secure: "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" before_install: git clone --depth 1 https://github.com/circulosmeos/gdown.pl && ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1 && tar -xzvf g16.tgz; -install: docker pull continuumio/miniconda3 -script: docker run -i -t -v $(pwd):/project -v ~/.cache/pip:/root/.cache/pip --env-file <(env | grep 'TRAVIS\|CI') continuumio/miniconda3 /bin/bash -c "chown -R root /root/.cache && pip install tox-conda && cd /project && export g16root=/project && source g16/bsd/g16.profile && tox -e py37" +install: docker pull njzjz/tox +script: docker run -i -t -v $(pwd):/project -v ~/.cache/pip:/root/.cache/pip --env-file <(env | grep 'TRAVIS\|CI') njzjz/tox /bin/bash -c "chown -R root /root/.cache && cd /project && export g16root=/project && source g16/bsd/g16.profile && tox -e py37" From a6a5cd661e52f72b2015dfc2479ce872207bcd9a Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sun, 5 May 2019 14:03:51 +0800 Subject: [PATCH 3/7] chore: revert travis (#25) --- .travis.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2f18a87..1733d44 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,10 +5,10 @@ sudo: false cache: directories: - $HOME/.cache/pip -services: docker env: global: + - PYTHON_VERSION=3.7 PIP_DEPENDENCIES="tox-conda tox-travis" CONDA_CHANNEL_PRIORITY=True CONDA_CHANNELS="conda-forge" - secure: "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" -before_install: git clone --depth 1 https://github.com/circulosmeos/gdown.pl && ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1 && tar -xzvf g16.tgz; -install: docker pull njzjz/tox -script: docker run -i -t -v $(pwd):/project -v ~/.cache/pip:/root/.cache/pip --env-file <(env | grep 'TRAVIS\|CI') njzjz/tox /bin/bash -c "chown -R root /root/.cache && cd /project && export g16root=/project && source g16/bsd/g16.profile && tox -e py37" +before_install: git clone --depth 1 https://github.com/circulosmeos/gdown.pl && ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1 && tar -xzvf g16.tgz && g16root=$(pwd) source g16/bsd/g16.profile +install: git clone --depth 1 git://github.com/astropy/ci-helpers.git && source ci-helpers/travis/setup_conda.sh +script: tox -e py37 From 113e6c23bcbdb8717e36a941d1e067ce633a2b7b Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Fri, 10 May 2019 00:30:50 +0800 Subject: [PATCH 4/7] chore: use CONDA_DEPENDENCIES (#26) --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 1733d44..d3e443e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,7 +7,7 @@ cache: - $HOME/.cache/pip env: global: - - PYTHON_VERSION=3.7 PIP_DEPENDENCIES="tox-conda tox-travis" CONDA_CHANNEL_PRIORITY=True CONDA_CHANNELS="conda-forge" + - PYTHON_VERSION=3.7 CONDA_DEPENDENCIES="tox-conda" CONDA_CHANNEL_PRIORITY=True CONDA_CHANNELS="conda-forge" - secure: "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" before_install: git clone --depth 1 https://github.com/circulosmeos/gdown.pl && ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1 && tar -xzvf g16.tgz && g16root=$(pwd) source g16/bsd/g16.profile install: git clone --depth 1 git://github.com/astropy/ci-helpers.git && source ci-helpers/travis/setup_conda.sh From 39de8d1143e23d76e2588a49ef6d51f755879e6f Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Fri, 24 May 2019 01:25:30 +0800 Subject: [PATCH 5/7] chore: update GitHub Actions (#28) * chore: update GitHub Actions * Update tox.ini * Delete .travis.yml --- .github/main.workflow | 28 +++++++++++++++------------- .travis.yml | 14 -------------- tox.ini | 2 +- 3 files changed, 16 insertions(+), 28 deletions(-) delete mode 100644 .travis.yml diff --git a/.github/main.workflow b/.github/main.workflow index a4e24f3..9fe047e 100644 --- a/.github/main.workflow +++ b/.github/main.workflow @@ -1,25 +1,27 @@ workflow "Release to pypi" { on = "release" - resolves = ["upload"] + resolves = ["publish"] } -action "check" { - uses = "ross/python-actions/setup-py/3.7@627646f618c3c572358bc7bc4fc413beb65fa50f" +action "publish" { + uses = "mariamrf/py-package-publish-action@master" args = "check" + secrets = ["TWINE_PASSWORD", "TWINE_USERNAME"] + env = { + PYTHON_VERSION = "3.7.3" + } } -action "sdist" { - uses = "ross/python-actions/setup-py/3.7@627646f618c3c572358bc7bc4fc413beb65fa50f" - args = "sdist" - needs = "check" +workflow "Test" { + on = "push" + resolves = ["Tox"] } -action "upload" { - uses = "ross/python-actions/twine@627646f618c3c572358bc7bc4fc413beb65fa50f" - args = "upload ./dist/aimdfragmentation-*.tar.gz" +action "Tox" { + uses = "njzjz/actions/tox-conda@master" secrets = [ - "TWINE_USERNAME", - "TWINE_PASSWORD", + "COVERALLS_REPO_TOKEN", + "CODECOV_TOKEN", + "GAUSSIANURL", ] - needs = "sdist" } diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index d3e443e..0000000 --- a/.travis.yml +++ /dev/null @@ -1,14 +0,0 @@ -language: c -os: - - linux -sudo: false -cache: - directories: - - $HOME/.cache/pip -env: - global: - - PYTHON_VERSION=3.7 CONDA_DEPENDENCIES="tox-conda" CONDA_CHANNEL_PRIORITY=True CONDA_CHANNELS="conda-forge" - - secure: "ryUltJvieQGY43Cd7nmSzKBWEZbywksbPOxJZ7Ig7Y428P8ML9u8zdKd9u2VT6JIdzpcfO0aKLuJfN4x+gL9G6DwJ2zIWDeou7fEcKtTcDc5SmVxhnErTFcgQ+7NTiLS2hufuQVZSpHGQ+GdSaDMa4y0/GRt/yxpKhBMa7dhd5L71hSi0Hs9BH6gJAuNfwaYhMOGy3GVBSvjKKFuH99u5KxaOUJ/R8Dd8evuQh5UgvWT1tpy0boPXCNLOEJbsXZtxqsTwezVoHoFHnuxiIHWABgAVye0DnIwjOCNQyGCey6HGYbKAx+lU7ldwmftEC8Tyody+VCbjz5DScEyxIEOLStzVFD6IFcJ6DgizXAFqZh2CXrBDo2e8IdkWgwZKrfDIh2YQntKc90isPimWamaYxHRh8rLorumWjeSt8D3CjdVoAOinTKLK+W3zK6YFymw1hgfj3h1aGxHBFlcuw4L7CzIc9u4duq5+VUZRQ4qSqPFIddd5N5vE0YBUJKCDm+LIk/YBY9udbM0vJDL4X9sKc02igbY4Mj6nm5TxuYMqHsos0CiDfhUJ8q3JEP6HKXunKIRw/AzF7BayYvVdHeZdSk8g1OhBIy4xi21d9aAs/6UpgTBw8lNVTC+SABtzH0iG574NYI9WmSt5r00qamQSsDnjJjZ5V1eM0LIf3Nk77A=" -before_install: git clone --depth 1 https://github.com/circulosmeos/gdown.pl && ./gdown.pl/gdown.pl $GAUSSIANURL 'g16.tgz'>/dev/null 2>&1 && tar -xzvf g16.tgz && g16root=$(pwd) source g16/bsd/g16.profile -install: git clone --depth 1 git://github.com/astropy/ci-helpers.git && source ci-helpers/travis/setup_conda.sh -script: tox -e py37 diff --git a/tox.ini b/tox.ini index 5016038..0ac3204 100644 --- a/tox.ini +++ b/tox.ini @@ -3,7 +3,7 @@ envlist = py37 [testenv] extras = test -passenv = GAUSS_* CI TRAVIS TRAVIS_* CODECOV_* +passenv = GAUSS_* CI TRAVIS TRAVIS_* CODECOV_* *_TOKEN deps = coveralls codecov>=1.4.0 From 4c74c818fc95f921560416879396c5cec367b818 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 14 Aug 2019 01:12:35 +0800 Subject: [PATCH 6/7] chore: converted main.workflow to Actions V2 yml files (#34) --- .github/workflows/push.yml | 14 ++++++++++++++ .github/workflows/release.yml | 15 +++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 .github/workflows/push.yml create mode 100644 .github/workflows/release.yml diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml new file mode 100644 index 0000000..62b4e97 --- /dev/null +++ b/.github/workflows/push.yml @@ -0,0 +1,14 @@ +on: push +name: Test +jobs: + tox: + name: Tox + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - name: Tox + uses: njzjz/actions/tox-conda@master + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} + GAUSSIANURL: ${{ secrets.GAUSSIANURL }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..98a0b81 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,15 @@ +on: release +name: Release to pypi +jobs: + publish: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - name: publish + uses: mariamrf/py-package-publish-action@master + env: + PYTHON_VERSION: 3.7.3 + TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }} + TWINE_USERNAME: ${{ secrets.TWINE_USERNAME }} + with: + args: check From 3d76bb222983ff86f1e845a00e986bb1b10d0d85 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Fri, 3 Jan 2020 16:06:54 -0500 Subject: [PATCH 7/7] fix: update use of openbabel (#39) * fix: update use of openbabel * Update push.yml * Update tox.ini * Update tox.ini --- .github/workflows/push.yml | 18 +++++++++++++++--- aimdfragmentation/frag.py | 10 +++++----- docs/README.md | 11 +++-------- tox.ini | 8 ++++---- 4 files changed, 27 insertions(+), 20 deletions(-) diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index 62b4e97..ecd6670 100644 --- a/.github/workflows/push.yml +++ b/.github/workflows/push.yml @@ -6,9 +6,21 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@master - - name: Tox - uses: njzjz/actions/tox-conda@master + - uses: actions/setup-python@v1 + with: + python-version: '3.7' + architecture: 'x64' + - run: pip install tox-conda + - run: git clone --depth 1 https://github.com/circulosmeos/gdown.pl + working-directory: /home/runner/work + - run: ./gdown.pl/gdown.pl $GAUSSIANURL "g16.tgz">/dev/null 2>&1 + env: + GAUSSIANURL: ${{ secrets.GAUSSIANURL }} + working-directory: /home/runner/work + - run: tar -xzvf g16.tgz + working-directory: /home/runner/work + - run: tox env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} - GAUSSIANURL: ${{ secrets.GAUSSIANURL }} + g16root: /home/runner/work diff --git a/aimdfragmentation/frag.py b/aimdfragmentation/frag.py index 5577c63..cab4ab9 100644 --- a/aimdfragmentation/frag.py +++ b/aimdfragmentation/frag.py @@ -90,12 +90,12 @@ def _readpdb(self): conv.SetInAndOutFormats('xyz', 'pdb') mol = openbabel.OBMol() conv.ReadFile(mol, self.xyzfilename) - pdbstring = conv.WriteString(mol) bond = [[] for x in range(self._natom)] - for line in pdbstring.split('\n'): - if line.startswith("CONECT"): - s = line.split() - bond[int(s[1])-1] += [int(x)-1 for x in s[2:]] + for b in openbabel.OBMolBondIter(mol): + s1 = b.GetBeginAtom().GetId() + s2 = b.GetEndAtom().GetId() + bond[s1].append(s2) + bond[s2].append(s1) # connect molecules self._mols = connectmolecule(bond) diff --git a/docs/README.md b/docs/README.md index 3cc7288..05c8e08 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,23 +1,18 @@ # Automated Fragmentation AIMD Calculation +[![DOI:10.26434/chemrxiv.11462160](https://zenodo.org/badge/DOI/10.1039/C9CP05091D.svg)](https://doi.org/10.26434/chemrxiv.11462160) [![python version](https://img.shields.io/pypi/pyversions/aimdfragmentation.svg?logo=python&logoColor=white)](https://pypi.org/project/aimdfragmentation) [![PyPI](https://img.shields.io/pypi/v/aimdfragmentation.svg)](https://pypi.org/project/aimdfragmentation) -[![Build Status](https://travis-ci.com/njzjz/aimdfragmentation.svg?branch=master)](https://travis-ci.com/njzjz/aimdfragmentation) -[![Coverage Status](https://coveralls.io/repos/github/njzjz/aimdfragmentation/badge.svg?branch=master)](https://coveralls.io/github/njzjz/aimdfragmentation?branch=master) [![codecov](https://codecov.io/gh/njzjz/aimdfragmentation/branch/master/graph/badge.svg)](https://codecov.io/gh/njzjz/aimdfragmentation) A automated fragmentation method for Ab Initio Molecular Dynamics (AIMD). +Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation, DOI: 10.26434/chemrxiv.11462160 + **Author**: Jinzhe Zeng **Email**: jzzeng@stu.ecnu.edu.cn -## Requirements -* [OpenBabel](https://github.com/openbabel/openbabel) -* [numpy](https://github.com/numpy/numpy) -* [ASE](https://gitlab.com/ase/ase) -* [GaussianRunner](https://github.com/njzjz/GaussianRunner) - ## Installation ### Using pip diff --git a/tox.ini b/tox.ini index 0ac3204..1e9e88c 100644 --- a/tox.ini +++ b/tox.ini @@ -3,19 +3,19 @@ envlist = py37 [testenv] extras = test -passenv = GAUSS_* CI TRAVIS TRAVIS_* CODECOV_* *_TOKEN +passenv = GAUSS_* CI TRAVIS TRAVIS_* CODECOV_* *_TOKEN g16root deps = coveralls codecov>=1.4.0 codacy-coverage conda_deps= openbabel - c-compiler - cxx-compiler conda_channels= conda-forge +whitelist_externals = + bash commands = - pytest --pyargs aimdfragmentation --cov {envsitepackagesdir}/aimdfragmentation -s + bash -c "source $g16root/g16/bsd/g16.profile; pytest --pyargs aimdfragmentation --cov {envsitepackagesdir}/aimdfragmentation -s" - coveralls - codecov - python-codacy-coverage -r coverage.xml