From b3f3f5f474e9dd407f69cd3763eba98257b88b00 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 1 Apr 2019 16:55:18 -0400 Subject: [PATCH 01/47] Fix quaternion --- sstmap/grid_water_analysis.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sstmap/grid_water_analysis.py b/sstmap/grid_water_analysis.py index 5d0fce0..be7ffcd 100644 --- a/sstmap/grid_water_analysis.py +++ b/sstmap/grid_water_analysis.py @@ -221,7 +221,7 @@ def calculate_euler_angles(self, water, coords): H_temp = np.zeros(3) H_temp[0] = ((w2*w2+x2*x2)-(y2*y2+z2*z2))*h1wat[0] - H_temp[0] = (2*(x2*y2 - w2*z2)*h1wat[1]) + H_temp[0] + H_temp[0] = (2*(x2*y2 + w2*z2)*h1wat[1]) + H_temp[0] H_temp[0] = (2*(x2*z2-w2*y2)*h1wat[2]) + H_temp[0] H_temp[1] = 2*(x2*y2 - w2*z2)* h1wat[0] @@ -235,7 +235,7 @@ def calculate_euler_angles(self, water, coords): H_temp2 = np.zeros(3,) H_temp2[0] = ((w2*w2+x2*x2)-(y2*y2+z2*z2))*h2wat[0] H_temp2[0] = (2*(x2*y2 + w2*z2)*h2wat[1]) + H_temp2[0] - H_temp2[0] = (2*(x2*z2-w2*y2)+h2wat[2]) +H_temp2[0] + H_temp2[0] = (2*(x2*z2-w2*y2)*h2wat[2]) +H_temp2[0] H_temp2[1] = 2*(x2*y2 - w2*z2) *h2wat[0] H_temp2[1] = ((w2*w2-x2*x2+y2*y2-z2*z2)*h2wat[1]) +H_temp2[1] From 3be289a8b55f34eff1a9acbf899ffb9385fbb0cd Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 1 Apr 2019 16:56:24 -0400 Subject: [PATCH 02/47] Update version --- sstmap/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sstmap/__init__.py b/sstmap/__init__.py index a17afa4..ccac5db 100644 --- a/sstmap/__init__.py +++ b/sstmap/__init__.py @@ -45,7 +45,7 @@ __license__ = "MIT" __maintainer__ = "Kamran Haider" __email__ = "kamranhaider.mb@gmail.com" -__version__ = "1.1.3" +__version__ = "1.1.4" from sstmap import site_water_analysis, grid_water_analysis, utils From 4bb1016ab726dcd9b41101c0a12e8d17c98e3bb3 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 1 Apr 2019 17:05:34 -0400 Subject: [PATCH 03/47] Fix version --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 451654f..698030f 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: sstmap - version: 1.1.3 + version: 1.1.4 source: path: ../../ From 20152bdb1d3e562dd3d9d36210c78438b4f5dd78 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 10:58:50 -0400 Subject: [PATCH 04/47] Update .travis.yml --- .travis.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 2e7270a..bc3c6b7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -48,10 +48,12 @@ env: # - python=3.4 CONDA_PY=34 - python=3.5 CONDA_PY=35 - python=3.6 CONDA_PY=36 + - python=3.7 CONDA_PY=37 + global: - PACKAGENAME="sstmap" - ORGNAME="solvationtools" after_success: - - source devtools/travis-ci/deploy_anaconda.sh \ No newline at end of file + - source devtools/travis-ci/deploy_anaconda.sh From 66ea9f1aece58484c48ba52cf8a27bbd70594879 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 11:02:53 -0400 Subject: [PATCH 05/47] Update .travis.yml --- .travis.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index bc3c6b7..4f4c7e7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -41,7 +41,6 @@ os: - osx - linux - env: matrix: - python=2.7 CONDA_PY=27 @@ -51,7 +50,6 @@ env: - python=3.7 CONDA_PY=37 global: - - PACKAGENAME="sstmap" - ORGNAME="solvationtools" From eda244bbec60410ffc52cb0cf228907e54d065fc Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 11:05:28 -0400 Subject: [PATCH 06/47] Change build status to master --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b8ce8b6..64ebfbf 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build Status](https://travis-ci.org/kamran-haider/SSTMap.svg?branch=v1.1_dev)](https://travis-ci.org/kamran-haider/SSTMap) +[![Build Status](https://travis-ci.org/kamran-haider/SSTMap.svg?branch=master)](https://travis-ci.org/kamran-haider/SSTMap) [![Anaconda-Server Badge](https://anaconda.org/solvationtools/sstmap/badges/installer/conda.svg)](https://conda.anaconda.org/solvationtools) [![Anaconda-Server Badge](https://anaconda.org/solvationtools/sstmap/badges/downloads.svg)](https://anaconda.org/solvationtools/sstmap) [![DOI for Citing SSTMap](https://img.shields.io/badge/DOI-10.1021%2Fj.jctc.2017.11.021-blue.svg)](http://doi.org/10.1021/acs.jctc.7b00592) From 72465384994d7a89f6bd8904fd263b26499288cc Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 11:12:49 -0400 Subject: [PATCH 07/47] Update meta.yaml --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 698030f..595730b 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -20,7 +20,7 @@ requirements: run: - python - libgcc - - numpy + - numpy 1.14.* - scipy - mdtraj - parmed From 98ae65d28a8c0c9c7a2c79f55af2d47c319e6925 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 11:27:25 -0400 Subject: [PATCH 08/47] Update meta.yaml --- devtools/conda-recipe/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 595730b..561840b 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -9,23 +9,23 @@ source: requirements: build: - python - - numpy 1.14.0 + - numpy 1.14.* - setuptools - gcc - toolchain - libgcc - - gsl 2.2.1 + - gsl >=2.2.1 - libopenblas run: - python - libgcc - - numpy 1.14.* + - numpy >=1.14 - scipy - mdtraj - parmed - matplotlib - - gsl 2.2.1 + - gsl >=2.2.1 - libopenblas #test: From b735b524985ae00a9a9246877fdf480b54f0419a Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 12:05:12 -0400 Subject: [PATCH 09/47] Move to toolchain3 --- devtools/conda-recipe/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 561840b..c1c38c7 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -12,20 +12,20 @@ requirements: - numpy 1.14.* - setuptools - gcc - - toolchain + - toolchain3 - libgcc - - gsl >=2.2.1 + - gsl 2.2.* - libopenblas run: - python - libgcc - - numpy >=1.14 + - numpy 1.14.* - scipy - mdtraj - parmed - matplotlib - - gsl >=2.2.1 + - gsl 2.2.* - libopenblas #test: From 24f57198321045b606aea2ea0f30fb1f4faeab24 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 2 Apr 2019 22:11:58 -0400 Subject: [PATCH 10/47] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 64ebfbf..d546f3e 100644 --- a/README.md +++ b/README.md @@ -38,8 +38,8 @@ You can also download the release package manually from GitHub, unzip it, naviga ```bash https://github.com/KurtzmanLab/SSTMap/archive/1.1.4.tar.gz or https://github.com/KurtzmanLab/SSTMap/archive/1.1.4.zip -tar -xvf 1.1.4.tar.gz or unzip 1.0.0.zip -cd SSTMap-1.0 +tar -xvf 1.1.4.tar.gz or unzip 1.1.4.zip +cd SSTMap-1.1.4 python setup.py install ``` Or you can clone the GitHub repository, navigate into the directory, and execute the command: @@ -109,7 +109,7 @@ Principal Developer(s) Co-Developers ------------- * Steven Ramsey -* Anthony Cruz Balberdi +* Anthony Cruz Balberdy * Tobias Wulsdorf Principal Investigators From 9a77533f901c4b1048d524b919180fe67f321258 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 3 Apr 2019 09:04:39 -0400 Subject: [PATCH 11/47] Only test python=2.7,3.5, and 3.6 --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 4f4c7e7..3cbacc4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -47,7 +47,6 @@ env: # - python=3.4 CONDA_PY=34 - python=3.5 CONDA_PY=35 - python=3.6 CONDA_PY=36 - - python=3.7 CONDA_PY=37 global: - PACKAGENAME="sstmap" From b245b98a4e4bc3708ecb2724c880de15d41f17df Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 3 Apr 2019 11:15:51 -0400 Subject: [PATCH 12/47] Trying toolchain2 --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 3cbacc4..d2f00d1 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,6 +19,7 @@ install: - source devtools/travis-ci/install_miniconda.sh - export PYTHONUNBUFFERED=true - export PATH=$HOME/miniconda/bin:$PATH + - conda config --add conda-forge/label/cf201901 - conda config --add channels conda-forge # hightest priority - conda config --add channels omnia From 86a20c42415f592aa00e20c22e39a8addd7d4a4c Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 3 Apr 2019 11:16:35 -0400 Subject: [PATCH 13/47] Trayin toolchain --- devtools/conda-recipe/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index c1c38c7..5f77080 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -12,9 +12,9 @@ requirements: - numpy 1.14.* - setuptools - gcc - - toolchain3 + - toolchain - libgcc - - gsl 2.2.* + - gsl 2.2.1 - libopenblas run: @@ -25,7 +25,7 @@ requirements: - mdtraj - parmed - matplotlib - - gsl 2.2.* + - gsl 2.2.1 - libopenblas #test: From 360eaef93db33cf7898dbe2ea8f195def60cbc8c Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 3 Apr 2019 11:21:23 -0400 Subject: [PATCH 14/47] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index d2f00d1..0b05cfd 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ install: - source devtools/travis-ci/install_miniconda.sh - export PYTHONUNBUFFERED=true - export PATH=$HOME/miniconda/bin:$PATH - - conda config --add conda-forge/label/cf201901 + - conda config --add channels conda-forge/label/cf201901 - conda config --add channels conda-forge # hightest priority - conda config --add channels omnia From 5aeb39de9fd9a776a71d14b29702e16cec7e35bd Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 3 Apr 2019 11:33:43 -0400 Subject: [PATCH 15/47] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 0b05cfd..ce040b7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ install: - source devtools/travis-ci/install_miniconda.sh - export PYTHONUNBUFFERED=true - export PATH=$HOME/miniconda/bin:$PATH - - conda config --add channels conda-forge/label/cf201901 + #- conda config --add channels conda-forge/label/cf201901 - conda config --add channels conda-forge # hightest priority - conda config --add channels omnia From 6e2f002bdc8a67893321688700b55e855e27b15a Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 3 Apr 2019 11:34:05 -0400 Subject: [PATCH 16/47] Update meta.yaml --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 5f77080..054968b 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -12,7 +12,7 @@ requirements: - numpy 1.14.* - setuptools - gcc - - toolchain + - toolchain3 - libgcc - gsl 2.2.1 - libopenblas From 19f9e85cf203925249b9ae87a75a9a32861d2483 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Thu, 4 Apr 2019 17:35:18 -0400 Subject: [PATCH 17/47] Test possible missing package in Travis --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index ce040b7..117e092 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,8 @@ addons: apt: sources: - ubuntu-toolchain-r-test + packages: + - libc6-dev before_install: - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi From fbba635de26707747ccead2a5d1fae059e5418a6 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 14:32:59 -0400 Subject: [PATCH 18/47] Fix for Travis CI --- setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f2b52d3..9d3a9d6 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,8 @@ extensions.append(Extension('_sstmap_ext', sources=['sstmap/_sstmap_ext.c'], include_dirs=[numpy.get_include()], - extra_link_args=['-lgsl','-lgslcblas'])) + extra_link_args=['-lgsl','-lgslcblas','-L/lib/x86_64-linux-gnu/'])) + extensions.append(Extension('_sstmap_entropy', sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'], language="c++")) From 10c37211430a681d996eb395c60bb4c998b7ea24 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 14:46:57 -0400 Subject: [PATCH 19/47] Update .travis.yml --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 117e092..8c96799 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,6 +30,8 @@ script: - conda config --add channels ${ORGNAME} # Create a test environment - conda create --quiet --yes -n test python=$python + # Activate root environment + - source activate root # Activate the test environment - source activate test # Build recipie From b5d2262658fbadaec9f59ae2af27529c30e52013 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 15:06:54 -0400 Subject: [PATCH 20/47] Travis fix 2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9d3a9d6..25d1772 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ extensions.append(Extension('_sstmap_ext', sources=['sstmap/_sstmap_ext.c'], include_dirs=[numpy.get_include()], - extra_link_args=['-lgsl','-lgslcblas','-L/lib/x86_64-linux-gnu/'])) + extra_link_args=['-lgsl','-lgslcblas','-L/usr/lib/x86_64-linux-gnu/'])) extensions.append(Extension('_sstmap_entropy', sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'], From bb767f765f4a37438d55adcfb471e9e407a37bb8 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 15:33:05 -0400 Subject: [PATCH 21/47] Travis fix 3 --- setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 25d1772..fcaca07 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,8 @@ extensions.append(Extension('_sstmap_ext', sources=['sstmap/_sstmap_ext.c'], include_dirs=[numpy.get_include()], - extra_link_args=['-lgsl','-lgslcblas','-L/usr/lib/x86_64-linux-gnu/'])) + extra_link_args=['-lgsl','-lgslcblas'], + libs_dirs=['/usr/lib/x86_64-linux-gnu/'])) extensions.append(Extension('_sstmap_entropy', sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'], From c18818ae4c4d60e72bc61bbe7b04b81d9c2a098c Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 15:41:47 -0400 Subject: [PATCH 22/47] Travis fix 4 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index fcaca07..e0e950d 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ sources=['sstmap/_sstmap_ext.c'], include_dirs=[numpy.get_include()], extra_link_args=['-lgsl','-lgslcblas'], - libs_dirs=['/usr/lib/x86_64-linux-gnu/'])) + library_dirs=['/usr/lib/x86_64-linux-gnu/'])) extensions.append(Extension('_sstmap_entropy', sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'], From 24203b5a36496a4f784f8d44ada05f8b226d339c Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 15:49:31 -0400 Subject: [PATCH 23/47] revert Travis --- setup.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/setup.py b/setup.py index e0e950d..343b08c 100644 --- a/setup.py +++ b/setup.py @@ -8,8 +8,7 @@ extensions.append(Extension('_sstmap_ext', sources=['sstmap/_sstmap_ext.c'], include_dirs=[numpy.get_include()], - extra_link_args=['-lgsl','-lgslcblas'], - library_dirs=['/usr/lib/x86_64-linux-gnu/'])) + extra_link_args=['-lgsl','-lgslcblas'])) extensions.append(Extension('_sstmap_entropy', sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'], From c16e03415a91aa1ac10278462182b18597790b07 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 15:51:33 -0400 Subject: [PATCH 24/47] conda-build last known good build --- devtools/conda-recipe/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 054968b..b5aab55 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -11,6 +11,7 @@ requirements: - python - numpy 1.14.* - setuptools + - conda-build 3.12.* - gcc - toolchain3 - libgcc From 3ac4ed306b4ca890e9e078baaa09c41192879cc8 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Mon, 8 Apr 2019 16:02:48 -0400 Subject: [PATCH 25/47] travis fix 5 --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 8c96799..7c820e9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -31,7 +31,7 @@ script: # Create a test environment - conda create --quiet --yes -n test python=$python # Activate root environment - - source activate root + #- source activate root # Activate the test environment - source activate test # Build recipie From f0158be20bbd71ac0f2edd30c77e1df45031673e Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 9 Apr 2019 08:43:40 -0400 Subject: [PATCH 26/47] Travis change 6 --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 7c820e9..3b7a11e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,8 +7,6 @@ addons: apt: sources: - ubuntu-toolchain-r-test - packages: - - libc6-dev before_install: - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi @@ -21,7 +19,7 @@ install: - source devtools/travis-ci/install_miniconda.sh - export PYTHONUNBUFFERED=true - export PATH=$HOME/miniconda/bin:$PATH - #- conda config --add channels conda-forge/label/cf201901 + - conda config --add channels conda-forge/label/cf201901 - conda config --add channels conda-forge # hightest priority - conda config --add channels omnia @@ -34,6 +32,8 @@ script: #- source activate root # Activate the test environment - source activate test + # Get conda info + - conda info # Build recipie - conda build devtools/conda-recipe # Install locally-built package From 4c40473d3af9826b216b5b595cb3e158304afd0a Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 9 Apr 2019 08:44:35 -0400 Subject: [PATCH 27/47] Update meta.yaml --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index b5aab55..1a6c48c 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -13,7 +13,7 @@ requirements: - setuptools - conda-build 3.12.* - gcc - - toolchain3 + - toolchain 2.1.6 - libgcc - gsl 2.2.1 - libopenblas From c55a9b5abf5cd40a2fe273ebfb18bd47ad07ea12 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 9 Apr 2019 09:01:37 -0400 Subject: [PATCH 28/47] toolchain changed --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 1a6c48c..bfa9cbb 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -13,7 +13,7 @@ requirements: - setuptools - conda-build 3.12.* - gcc - - toolchain 2.1.6 + - toolchain 2.1.* - libgcc - gsl 2.2.1 - libopenblas From 7387b4cf4790dd1aa6e7384f11655794c1db6554 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 9 Apr 2019 09:11:50 -0400 Subject: [PATCH 29/47] Get env info to reproduce Travis --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 3b7a11e..eb31b4d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -34,6 +34,8 @@ script: - source activate test # Get conda info - conda info + # Get environment info + - conda list --explicit # Build recipie - conda build devtools/conda-recipe # Install locally-built package From 62433d47a8f8aba2365ff2664dc145f34f5dfcb9 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 16 Apr 2019 08:23:30 -0400 Subject: [PATCH 30/47] Try fix from Travis Help email --- .travis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index eb31b4d..46f4baa 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,7 +37,8 @@ script: # Get environment info - conda list --explicit # Build recipie - - conda build devtools/conda-recipe + #- conda build devtools/conda-recipe + - conda-build devtools/conda-recipe -c conda-forge/label/gcc7 # Install locally-built package - conda install --yes --quiet --use-local ${PACKAGENAME} #- conda install --yes --quiet pip nose nose-timer From 12d9456862547ff78abc9e3e5f3b7531479a245a Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 16 Apr 2019 22:12:56 -0400 Subject: [PATCH 31/47] remove ubuntu toolchain --- .travis.yml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index 46f4baa..525d7db 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,11 +3,6 @@ language: C sudo: false -addons: - apt: - sources: - - ubuntu-toolchain-r-test - before_install: - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi @@ -19,7 +14,6 @@ install: - source devtools/travis-ci/install_miniconda.sh - export PYTHONUNBUFFERED=true - export PATH=$HOME/miniconda/bin:$PATH - - conda config --add channels conda-forge/label/cf201901 - conda config --add channels conda-forge # hightest priority - conda config --add channels omnia @@ -37,8 +31,8 @@ script: # Get environment info - conda list --explicit # Build recipie - #- conda build devtools/conda-recipe - - conda-build devtools/conda-recipe -c conda-forge/label/gcc7 + - conda build devtools/conda-recipe + #- conda-build devtools/conda-recipe -c conda-forge/label/gcc7 # Install locally-built package - conda install --yes --quiet --use-local ${PACKAGENAME} #- conda install --yes --quiet pip nose nose-timer From 4d14c62dba486fbc324c7634f2a6720ba302ff8f Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Tue, 16 Apr 2019 22:22:18 -0400 Subject: [PATCH 32/47] toolchain3 --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index bfa9cbb..b5aab55 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -13,7 +13,7 @@ requirements: - setuptools - conda-build 3.12.* - gcc - - toolchain 2.1.* + - toolchain3 - libgcc - gsl 2.2.1 - libopenblas From 5214a4098e6a7d52dd115217010f52f6d26b0f16 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 17 Apr 2019 08:29:57 -0400 Subject: [PATCH 33/47] specify versions --- devtools/conda-recipe/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index b5aab55..9e1f233 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -10,13 +10,15 @@ requirements: build: - python - numpy 1.14.* - - setuptools + - setuptools 40.4.* - conda-build 3.12.* - - gcc + - gcc 4.8.* - toolchain3 - - libgcc + - libgcc 7.2.* - gsl 2.2.1 - - libopenblas + - libopenblas 0.3.* + - libgcc-ng 7.2.* + - libstdcxx-ng 7.2.* run: - python From 2de2b0c6814bfa919d0b382b998d6984f088ec3a Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 17 Apr 2019 08:36:15 -0400 Subject: [PATCH 34/47] Update meta.yaml --- devtools/conda-recipe/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 9e1f233..9c213de 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -14,11 +14,11 @@ requirements: - conda-build 3.12.* - gcc 4.8.* - toolchain3 - - libgcc 7.2.* + - libgcc 7.3.* - gsl 2.2.1 - libopenblas 0.3.* - - libgcc-ng 7.2.* - - libstdcxx-ng 7.2.* + - libgcc-ng 7.3.* + - libstdcxx-ng 7.3.* run: - python From 11d01b6bcc1f503cf7eb79b9a18b26e0c5e7d697 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Wed, 17 Apr 2019 09:10:10 -0400 Subject: [PATCH 35/47] Update .travis.yml --- .travis.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.travis.yml b/.travis.yml index 525d7db..0554252 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,6 +3,11 @@ language: C sudo: false +addons: + apt: + sources: + - ubuntu-toolchain-r-test + before_install: - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi From 9ebc0b735e5974b16e8469b2955c6488619cf700 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Thu, 23 May 2019 15:10:57 -0400 Subject: [PATCH 36/47] fix problem with libgcc --- devtools/conda-recipe/meta.yaml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 9c213de..63aa359 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -9,21 +9,21 @@ source: requirements: build: - python - - numpy 1.14.* - - setuptools 40.4.* - - conda-build 3.12.* - - gcc 4.8.* + - numpy + - setuptools + - conda-build + - gcc - toolchain3 - - libgcc 7.3.* + - libgcc - gsl 2.2.1 - - libopenblas 0.3.* - - libgcc-ng 7.3.* - - libstdcxx-ng 7.3.* + - libopenblas + - libgcc-ng + - libstdcxx-ng run: - python - libgcc - - numpy 1.14.* + - numpy - scipy - mdtraj - parmed From cdae1d4f642858531ec9501020c9ee4cc6c1a53a Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Thu, 23 May 2019 16:47:46 -0400 Subject: [PATCH 37/47] remove CC --- Makefile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Makefile b/Makefile index d4ec700..b498d76 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,3 @@ -CC = g++ SOURCEDIR = ./sstmap INSTALLDIR = ~/anaconda2/bin bruteclust: $(SOURCEDIR)/make_clust_brute.cpp @@ -18,4 +17,4 @@ clean: rm -f kdhsa102 rm -f 6dimprobable -test: pytest -m tests \ No newline at end of file +test: pytest -m tests From 2d3fbbfb0d0957828cff9379c057a1aa6fe50199 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Thu, 23 May 2019 17:41:57 -0400 Subject: [PATCH 38/47] mod ld from conda --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 0554252..8195ae2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,6 +23,7 @@ install: - conda config --add channels omnia script: + - mv $HOME/miniconda/compiler_compat/ld $HOME/miniconda/compiler_compat/ld2 # Add org channel - conda config --add channels ${ORGNAME} # Create a test environment From a873dc6fce68ecbb129153a564e162c2488523a4 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Thu, 23 May 2019 17:55:44 -0400 Subject: [PATCH 39/47] try 2 ld --- .travis.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 8195ae2..c0542f6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,7 +23,6 @@ install: - conda config --add channels omnia script: - - mv $HOME/miniconda/compiler_compat/ld $HOME/miniconda/compiler_compat/ld2 # Add org channel - conda config --add channels ${ORGNAME} # Create a test environment @@ -34,6 +33,9 @@ script: - source activate test # Get conda info - conda info + # Remove conda ld + - mv $PREFIX/compiler_compat/ld $PREFIX/compiler_compat/ld2 + - mv $HOME/miniconda/compiler_compat/ld $HOME/miniconda/compiler_compat/ld2 # Get environment info - conda list --explicit # Build recipie From da15da4ba40551131c8817cec6cd5c8673019ec2 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 08:14:59 -0400 Subject: [PATCH 40/47] rename ld --- devtools/travis-ci/install_miniconda.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/travis-ci/install_miniconda.sh b/devtools/travis-ci/install_miniconda.sh index 215e9f3..251a979 100644 --- a/devtools/travis-ci/install_miniconda.sh +++ b/devtools/travis-ci/install_miniconda.sh @@ -22,4 +22,5 @@ export PIP_ARGS="-U" export PATH=$MINICONDA_HOME/bin:$PATH conda update --yes conda conda install --yes conda-build jinja2 anaconda-client +mv $MINICONDA_HOME/compiler_compat/ld $MINICONDA_HOME/compiler_compat/ld2 popd From e7f1a5a37a4a99fd7e75ca4112f673acae395532 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 10:08:29 -0400 Subject: [PATCH 41/47] change way to get compiler --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 63aa359..70157c1 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -12,7 +12,7 @@ requirements: - numpy - setuptools - conda-build - - gcc + - {{ compiler('c') }} - toolchain3 - libgcc - gsl 2.2.1 From 0f184280dabd5ec71bb444614364196b75d82bf9 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 10:19:52 -0400 Subject: [PATCH 42/47] no need to rename ld --- .travis.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index c0542f6..0554252 100644 --- a/.travis.yml +++ b/.travis.yml @@ -33,9 +33,6 @@ script: - source activate test # Get conda info - conda info - # Remove conda ld - - mv $PREFIX/compiler_compat/ld $PREFIX/compiler_compat/ld2 - - mv $HOME/miniconda/compiler_compat/ld $HOME/miniconda/compiler_compat/ld2 # Get environment info - conda list --explicit # Build recipie From 5f8469ab34060e50d301c613f664f72bca0f1205 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 10:20:41 -0400 Subject: [PATCH 43/47] no need to rename ld --- devtools/travis-ci/install_miniconda.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/devtools/travis-ci/install_miniconda.sh b/devtools/travis-ci/install_miniconda.sh index 251a979..215e9f3 100644 --- a/devtools/travis-ci/install_miniconda.sh +++ b/devtools/travis-ci/install_miniconda.sh @@ -22,5 +22,4 @@ export PIP_ARGS="-U" export PATH=$MINICONDA_HOME/bin:$PATH conda update --yes conda conda install --yes conda-build jinja2 anaconda-client -mv $MINICONDA_HOME/compiler_compat/ld $MINICONDA_HOME/compiler_compat/ld2 popd From b743edb99a8f00c4ef2cb37dc642e9806820e25b Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 12:02:16 -0400 Subject: [PATCH 44/47] variant 2 --- devtools/conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 70157c1..242501c 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -12,7 +12,7 @@ requirements: - numpy - setuptools - conda-build - - {{ compiler('c') }} + - {{ compiler() }} - toolchain3 - libgcc - gsl 2.2.1 From 5621c2bac3958ef89f1ec0886c3ac9f8207b5f17 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 13:10:26 -0400 Subject: [PATCH 45/47] add host --- devtools/conda-recipe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 242501c..7b06f43 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -8,18 +8,18 @@ source: requirements: build: + - {{ compiler('c') }} + host: - python - numpy - setuptools - conda-build - - {{ compiler() }} - toolchain3 - libgcc - gsl 2.2.1 - libopenblas - libgcc-ng - libstdcxx-ng - run: - python - libgcc From 81d2b595901ba60a7d93bdd2e76ee7fd2f17732f Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 13:33:20 -0400 Subject: [PATCH 46/47] trigger build --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index d546f3e..dcf3c05 100644 --- a/README.md +++ b/README.md @@ -54,6 +54,7 @@ git checkout tags/1.1.4 python setup.py install ``` **For the developmental version:** + ``` python setup.py install ``` From cbc1ac449471e968388b1979e4971323a8a62360 Mon Sep 17 00:00:00 2001 From: Anthony Cruz Date: Fri, 24 May 2019 13:46:49 -0400 Subject: [PATCH 47/47] adding cxx compiler --- devtools/conda-recipe/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 7b06f43..325f751 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -9,6 +9,7 @@ source: requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - numpy