diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 73450fd03..2124a2971 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -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: diff --git a/actions/upload_package.sh b/actions/upload_package.sh index 3d8a4e1ff..bb058632e 100755 --- a/actions/upload_package.sh +++ b/actions/upload_package.sh @@ -29,8 +29,8 @@ 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 \ @@ -38,16 +38,14 @@ if [ "$LABEL" = "main" ]; then --label main \ --label dev \ --force \ - "$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!" diff --git a/recipes/fkcombu/LICENSE b/recipes/fkcombu/LICENSE new file mode 100644 index 000000000..529b0dab5 --- /dev/null +++ b/recipes/fkcombu/LICENSE @@ -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. diff --git a/recipes/fkcombu/build.sh b/recipes/fkcombu/build.sh new file mode 100644 index 000000000..2c09cb50d --- /dev/null +++ b/recipes/fkcombu/build.sh @@ -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 diff --git a/recipes/fkcombu/meta.yaml b/recipes/fkcombu/meta.yaml new file mode 100644 index 000000000..dc6dc1890 --- /dev/null +++ b/recipes/fkcombu/meta.yaml @@ -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 diff --git a/recipes/sire/template.yaml b/recipes/sire/template.yaml index 02dcfc177..d80878ecf 100644 --- a/recipes/sire/template.yaml +++ b/recipes/sire/template.yaml @@ -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