From bfc520900384b4e477613a8c409f50689550012d Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 15:54:27 -0500 Subject: [PATCH 01/13] try building --- circle.yml | 11 +++++++++++ devtools/Dockerfile | 9 +++++++++ devtools/circleci/install_miniconda.sh | 30 ++++++++++++++++++++++++++++++ 3 files changed, 50 insertions(+) create mode 100644 circle.yml create mode 100644 devtools/Dockerfile create mode 100644 devtools/circleci/install_miniconda.sh diff --git a/circle.yml b/circle.yml new file mode 100644 index 00000000..ec22b1fd --- /dev/null +++ b/circle.yml @@ -0,0 +1,11 @@ +machine: + services: + - docker + +dependencies: + override: + - docker pull ambermd/manylinux-extra + +test: + override: + - docker build -t nglview:dev devtools/ diff --git a/devtools/Dockerfile b/devtools/Dockerfile new file mode 100644 index 00000000..a6714ad7 --- /dev/null +++ b/devtools/Dockerfile @@ -0,0 +1,9 @@ +FROM ambermd/manylinux-extra + +# To get the AmberTools16.tar.bz file, fill out the form +# at the site below and click Download. +ADD ../nglview /root/ + +RUN cd /root/nglview \ + && sh devtools/circleci/install_miniconda.sh \ + && python setup.py install diff --git a/devtools/circleci/install_miniconda.sh b/devtools/circleci/install_miniconda.sh new file mode 100644 index 00000000..003ab785 --- /dev/null +++ b/devtools/circleci/install_miniconda.sh @@ -0,0 +1,30 @@ +#!/bin/sh + +miniconda=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh +wget $miniconda -O miniconda.sh +bash miniconda.sh -b +export PATH=/root/miniconda3/bin:$PATH +conda update --yes --all +conda install --yes conda-build anaconda-client numpy matplotlib +conda info +conda install --yes jupyter notebook nose numpy mock coverage cython netcdf4 +# pytraj +pip install pytraj +# mdanalysis +conda config --add channels MDAnalysis +conda install mdanalysis -c kain88-de --yes +# mdtraj +conda install mdtraj -c omnia --yes +# ParmEd +pip install https://github.com/ParmEd/ParmEd/archive/2.5.1.tar.gz +# ase +pip install https://github.com/hainm/ase/archive/3.11.0.tar.gz +# simpletraj +pip install git+https://github.com/arose/simpletraj +# pytest +pip install pytest +pip install pytest-cov +# coveralls +pip install coveralls +# rdkit +conda install rdkit -c rdkit --yes From 99d79b865a02e271bb12957d3b84439a874dd181 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 15:57:23 -0500 Subject: [PATCH 02/13] add CMD --- devtools/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/Dockerfile b/devtools/Dockerfile index a6714ad7..66ff3ca5 100644 --- a/devtools/Dockerfile +++ b/devtools/Dockerfile @@ -7,3 +7,4 @@ ADD ../nglview /root/ RUN cd /root/nglview \ && sh devtools/circleci/install_miniconda.sh \ && python setup.py install +CMD ["nglview", "demo"] From afa9e1a67ec6664e9847578059e34c3cc1ab3354 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:23:25 -0500 Subject: [PATCH 03/13] docker --- devtools/Dockerfile => Dockerfile | 2 +- setup.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename devtools/Dockerfile => Dockerfile (92%) diff --git a/devtools/Dockerfile b/Dockerfile similarity index 92% rename from devtools/Dockerfile rename to Dockerfile index 66ff3ca5..f62ac150 100644 --- a/devtools/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ FROM ambermd/manylinux-extra # To get the AmberTools16.tar.bz file, fill out the form # at the site below and click Download. -ADD ../nglview /root/ +ADD . /root/nglview RUN cd /root/nglview \ && sh devtools/circleci/install_miniconda.sh \ diff --git a/setup.py b/setup.py index d04db6ed..c5fd458a 100644 --- a/setup.py +++ b/setup.py @@ -42,7 +42,7 @@ def enable_extentions(): from notebook.nbextensions import enable_nbextension_python enable_nbextension_python('widgetsnbextension') enable_nbextension_python('nglview') - except Exception as e: + except: print('Failed to enable extensions {}'.format(e)) def js_prerelease(command, strict=False): @@ -57,7 +57,7 @@ def run(self): try: self.distribution.run_command('jsdeps') - except Exception as e: + except: missing = [t for t in jsdeps.targets if not os.path.exists(t)] if strict or missing: log.warn('rebuilding js and css failed') From c3954645f867db7c163b34ba8a2c8ea347c20155 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:26:12 -0500 Subject: [PATCH 04/13] absolute path to miniconda --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f62ac150..012cb6a6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,5 +6,5 @@ ADD . /root/nglview RUN cd /root/nglview \ && sh devtools/circleci/install_miniconda.sh \ - && python setup.py install + && /root/miniconda3/bin/python setup.py install CMD ["nglview", "demo"] From e5c70574cae55c30c437bdb05f3299697d2dcb55 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:26:52 -0500 Subject: [PATCH 05/13] . --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index ec22b1fd..0f6c2ad1 100644 --- a/circle.yml +++ b/circle.yml @@ -8,4 +8,4 @@ dependencies: test: override: - - docker build -t nglview:dev devtools/ + - docker build -t nglview:dev . From 896f1e65463434edf38581e97a312e674190bc97 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:28:56 -0500 Subject: [PATCH 06/13] simplify --- devtools/circleci/install_miniconda.sh | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/devtools/circleci/install_miniconda.sh b/devtools/circleci/install_miniconda.sh index 003ab785..d88cc9fd 100644 --- a/devtools/circleci/install_miniconda.sh +++ b/devtools/circleci/install_miniconda.sh @@ -16,15 +16,10 @@ conda install mdanalysis -c kain88-de --yes # mdtraj conda install mdtraj -c omnia --yes # ParmEd -pip install https://github.com/ParmEd/ParmEd/archive/2.5.1.tar.gz +conda install -c ambermd parmed --yes # ase pip install https://github.com/hainm/ase/archive/3.11.0.tar.gz # simpletraj pip install git+https://github.com/arose/simpletraj -# pytest -pip install pytest -pip install pytest-cov -# coveralls -pip install coveralls # rdkit -conda install rdkit -c rdkit --yes +# conda install rdkit -c rdkit --yes From c8a08e56a19069be09270df00befd7b1ff1bccaa Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:29:52 -0500 Subject: [PATCH 07/13] turn off CMD for now --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 012cb6a6..14e21944 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,4 +7,4 @@ ADD . /root/nglview RUN cd /root/nglview \ && sh devtools/circleci/install_miniconda.sh \ && /root/miniconda3/bin/python setup.py install -CMD ["nglview", "demo"] +# CMD ["nglview", "demo"] From 14840a19b81b82f9b954f38c87a729d52afa7413 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:37:30 -0500 Subject: [PATCH 08/13] use conda-forge for some stuff --- Dockerfile | 3 ++- devtools/circleci/install_miniconda.sh | 3 +++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 14e21944..0741a9f6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,5 @@ -FROM ambermd/manylinux-extra +# FROM ambermd/manylinux-extra +FROM condaforge/linux-anvil # To get the AmberTools16.tar.bz file, fill out the form # at the site below and click Download. diff --git a/devtools/circleci/install_miniconda.sh b/devtools/circleci/install_miniconda.sh index d88cc9fd..f0b7c8da 100644 --- a/devtools/circleci/install_miniconda.sh +++ b/devtools/circleci/install_miniconda.sh @@ -23,3 +23,6 @@ pip install https://github.com/hainm/ase/archive/3.11.0.tar.gz pip install git+https://github.com/arose/simpletraj # rdkit # conda install rdkit -c rdkit --yes + +# update a bunch of stuff +conda install --yes -c conda-forge ipywidgets notebook pyzmq From c27687a70ce8bf7b617d6360aea1dac8d237f2af Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 16:58:02 -0500 Subject: [PATCH 09/13] yum yum --- devtools/circleci/install_miniconda.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/devtools/circleci/install_miniconda.sh b/devtools/circleci/install_miniconda.sh index f0b7c8da..792f0f15 100644 --- a/devtools/circleci/install_miniconda.sh +++ b/devtools/circleci/install_miniconda.sh @@ -1,5 +1,9 @@ #!/bin/sh +yum install -y \ + wget \ + unzip + miniconda=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget $miniconda -O miniconda.sh bash miniconda.sh -b From abe40b2701c4e529ac3fdb0eda3b977de7ad4f65 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 17:34:31 -0500 Subject: [PATCH 10/13] use conda from conda-forge --- circle.yml | 2 +- devtools/circleci/install_miniconda.sh | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/circle.yml b/circle.yml index 0f6c2ad1..d4165454 100644 --- a/circle.yml +++ b/circle.yml @@ -4,7 +4,7 @@ machine: dependencies: override: - - docker pull ambermd/manylinux-extra + - docker pull condaforge/linux-anvil test: override: diff --git a/devtools/circleci/install_miniconda.sh b/devtools/circleci/install_miniconda.sh index 792f0f15..a71dadb1 100644 --- a/devtools/circleci/install_miniconda.sh +++ b/devtools/circleci/install_miniconda.sh @@ -4,10 +4,11 @@ yum install -y \ wget \ unzip -miniconda=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -wget $miniconda -O miniconda.sh -bash miniconda.sh -b -export PATH=/root/miniconda3/bin:$PATH +# miniconda=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh +# wget $miniconda -O miniconda.sh +# bash miniconda.sh -b +# export PATH=/root/miniconda3/bin:$PATH +export PATH=/opt/conda/bin/:$PATH conda update --yes --all conda install --yes conda-build anaconda-client numpy matplotlib conda info From 34d4a8c48dccb47e18e7ef082eb66d0c2c866741 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 17:36:36 -0500 Subject: [PATCH 11/13] turn off simpltraj --- devtools/circleci/install_miniconda.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/devtools/circleci/install_miniconda.sh b/devtools/circleci/install_miniconda.sh index a71dadb1..3d0d4ec1 100644 --- a/devtools/circleci/install_miniconda.sh +++ b/devtools/circleci/install_miniconda.sh @@ -25,7 +25,8 @@ conda install -c ambermd parmed --yes # ase pip install https://github.com/hainm/ase/archive/3.11.0.tar.gz # simpletraj -pip install git+https://github.com/arose/simpletraj +# turn off for now since this package requires install from source code. +# pip install git+https://github.com/arose/simpletraj # rdkit # conda install rdkit -c rdkit --yes From b56348ef349981a959a5157dba16ad5a39151090 Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 17:37:17 -0500 Subject: [PATCH 12/13] use opt --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0741a9f6..7586928c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,5 +7,5 @@ ADD . /root/nglview RUN cd /root/nglview \ && sh devtools/circleci/install_miniconda.sh \ - && /root/miniconda3/bin/python setup.py install + && /opt/conda/bin/python setup.py install # CMD ["nglview", "demo"] From df4357638059e68f33e30bb5957472eb7268979b Mon Sep 17 00:00:00 2001 From: Hai Nguyen Date: Mon, 21 Nov 2016 20:07:08 -0500 Subject: [PATCH 13/13] Update Dockerfile --- Dockerfile | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7586928c..74d5d19a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,5 @@ -# FROM ambermd/manylinux-extra FROM condaforge/linux-anvil - -# To get the AmberTools16.tar.bz file, fill out the form -# at the site below and click Download. ADD . /root/nglview - RUN cd /root/nglview \ && sh devtools/circleci/install_miniconda.sh \ && /opt/conda/bin/python setup.py install