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Merge branch 'devel' of https://github.com/michellab/Sire into devel
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Christopher Woods authored and Christopher Woods committed Feb 1, 2022
2 parents a5fd825 + 1c3df5d commit d856a1e
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2 changes: 1 addition & 1 deletion .github/workflows/main.yaml
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Expand Up @@ -36,7 +36,7 @@ jobs:
if: github.event_name == 'pull_request'
- name: Setup Conda
shell: bash -l {0}
run: conda install -y conda-build anaconda-client
run: conda install -y -c conda-forge conda-build anaconda-client
- name: Update Conda recipe
run: Sire/actions/update_recipe.sh
env:
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10 changes: 4 additions & 6 deletions actions/upload_package.sh
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Expand Up @@ -29,25 +29,23 @@ fi

# Upload the packages to the michellab channel on Anaconda Cloud.

# Label release packages with main and dev so that dev is at least as new as main.
# Uncomment the libcpuid package upload as and when there are new releases.
# Label release packages with main and dev so that dev is at least
# as new as main.
if [ "$LABEL" = "main" ]; then
anaconda \
--token "$ANACONDA_TOKEN" upload \
--user michellab \
--label main \
--label dev \
--force \
"$CONDA_BLD"/"$OS"/sire-*
# "$CONDA_BLD"/"$OS"/libcpuid-*
"$CONDA_BLD"/"$OS"/*.bz2
else
anaconda \
--token "$ANACONDA_TOKEN" upload \
--user michellab \
--label dev \
--force \
"$CONDA_BLD"/"$OS"/sire-*
# "$CONDA_BLD"/"$OS"/libcpuid-*
"$CONDA_BLD"/"$OS"/*.bz2
fi

echo "Package uploaded!"
24 changes: 24 additions & 0 deletions recipes/fkcombu/LICENSE
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@@ -0,0 +1,24 @@
Copyright (c) 2018, Takeshi Kawabata
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the Institute for Protein Research, Osaka University
nor the names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL Takeshi Kawabata BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18 changes: 18 additions & 0 deletions recipes/fkcombu/build.sh
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@@ -0,0 +1,18 @@
#!/usr/bin/env bash

set -ex

if [ "$(uname)" == "Linux" ]; then
# Update the C compiler on Linux.
sed -i "s#gcc#$CC#g" Makefile.fkcombu
else
# Ignore implicit function declaration errors on macOS.
sed -i.bak -e "s#Wall#Wno-implicit-function-declaration#g" Makefile.fkcombu
fi

# Build FKCOMBU.
make -f Makefile.fkcombu

# Copy the FKCOMBU executable to the bin directory.
mkdir ${PREFIX}/bin
cp -a ../fkcombu ${PREFIX}/bin
35 changes: 35 additions & 0 deletions recipes/fkcombu/meta.yaml
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@@ -0,0 +1,35 @@
{% set name = "fkcombu" %}
{% set version = "2020.04.14" %}

package:
name: {{ name }}
version: {{ version }}

source:
url: https://pdbj.org/kcombu/cgi-bin/dwnld_src_file.cgi?filename=kcombu-src-20200414.tar.gz
sha256: 2394029273667260817ff14ff0ed9e38cd3fd9f0756a48456c55a53c47a39d75

build:
number: 0

requirements:
build:
- {{ compiler('c') }}
- make

test:
commands:
- test -f $PREFIX/bin/fkcombu

about:
home: https://pdbj.org/kcombu/doc/README_fkcombu.html
license: BSD-3-Clause
license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE'
summary: A tool for flexible transformation of a target molecule onto a reference molecule.
dev_url: https://pdbj.org/kcombu/doc/README_fkcombu.html
doc_url: https://pdbj.org/kcombu/doc/README_fkcombu.html
description: A tool for flexible transformation of a target molecule onto a reference molecule.

extra:
recipe-maintainers:
- lohedges
16 changes: 16 additions & 0 deletions recipes/sire/template.yaml
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Expand Up @@ -32,6 +32,22 @@ requirements:
- qt
- tbb-devel
- tbb
# Add BioSimSpace run dependencies so Sire dependencies
# are resolved in a compatible way.
- configargparse
- fkcombu
- mdtraj
- mdanalysis
- nglview
- openff-toolkit-base
- parmed
- pydot
- pygtail
- pypdb
- pytest
- pyyaml
- rdkit
- watchdog
run:
- boost
- gsl
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