Merge branch 'devel' of https://github.com/michellab/Sire into devel

Author: Christopher Woods

.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:

actions/upload_package.sh

@@ -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!"

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.

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

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

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