From 45121dd9003b8ef9211cd4e4fdfc3c8ab1c96fe8 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Tue, 26 Jul 2016 11:57:02 +0200 Subject: [PATCH] Fix file capitalization in notebooks --- docker_images/DockerMake-dev.yml | 8 ++++++++ docker_images/DockerMake.yml | 8 ++++---- .../.building/Example 3. Simulate HIV Protease.ipynb | 2 +- moldesign/_notebooks/.building/Header.ipynb | 2 +- .../_notebooks/Example 1. Build and simulate DNA.ipynb | 2 +- .../_notebooks/Example 2. Running Quantum Chemistry.ipynb | 2 +- moldesign/_notebooks/Getting Started.ipynb | 6 +++--- moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb | 2 +- 8 files changed, 20 insertions(+), 12 deletions(-) diff --git a/docker_images/DockerMake-dev.yml b/docker_images/DockerMake-dev.yml index c3cba37..0321ed6 100644 --- a/docker_images/DockerMake-dev.yml +++ b/docker_images/DockerMake-dev.yml @@ -56,3 +56,11 @@ dev_deploys: && pip install git+https://github.com/Autodesk/py-cloud-compute-cannon@dev ENTRYPOINT python -m moldesign intro +master_deploy: + requires: + - deploy_test_base + description: Install from master branch + build: | + RUN pip install biopython jupyter + RUN pip install git+https://github.com/Autodesk/molecular-design-toolkit@master + diff --git a/docker_images/DockerMake.yml b/docker_images/DockerMake.yml index 9d5687d..35429ca 100644 --- a/docker_images/DockerMake.yml +++ b/docker_images/DockerMake.yml @@ -79,7 +79,7 @@ devtools: ############################################ # moldesign -# Note - this image installs from GITHUB MASTER so that we can test it before pushing to pypi +# Note - this image installs from github so we can test it before submitting to pypi moldesign: requires: # TODO: remove biopython dependency (it's in C ...) - python_install @@ -87,7 +87,7 @@ moldesign: build: | RUN apt-get update && apt-get install -y gcc gfortran python-dev git \ && pip install biopython \ - && pip install git+https://github.com/Autodesk/molecular-design-toolkit@master \ + && pip install git+https://github.com/Autodesk/molecular-design-toolkit@0.7.2 \ && apt-get -y remove --purge gcc gfortran python-dev git \ && apt-get -y autoremove --purge \ && apt-get -y clean @@ -97,7 +97,7 @@ pyccc: requires: - python_install build: | - RUN pip install pyccc + RUN pip install pyccc==0.6.4 nbmolviz: @@ -105,7 +105,7 @@ nbmolviz: - python_install build: | RUN pip install nbmolviz - RUN jupyter nbextension enable --python --sys-prefix nbmolviz && + RUN jupyter nbextension enable --python --sys-prefix nbmolviz==0.6.5 && jupyter nbextension enable --python --sys-prefix widgetsnbextensions diff --git a/moldesign/_notebooks/.building/Example 3. Simulate HIV Protease.ipynb b/moldesign/_notebooks/.building/Example 3. Simulate HIV Protease.ipynb index 3713eaf..efe8801 100644 --- a/moldesign/_notebooks/.building/Example 3. Simulate HIV Protease.ipynb +++ b/moldesign/_notebooks/.building/Example 3. Simulate HIV Protease.ipynb @@ -7,7 +7,7 @@ "\n", "About      Forum      Issues      Tutorials      Documentation\n", "\n", - "![Molecular Design Toolkit](img/top.png)\n", + "![Molecular Design Toolkit](img/Top.png)\n", "
\n", "\n", "

Example 3: Simulating HIV Protease

\n", diff --git a/moldesign/_notebooks/.building/Header.ipynb b/moldesign/_notebooks/.building/Header.ipynb index 9bc40f9..b07f7fb 100644 --- a/moldesign/_notebooks/.building/Header.ipynb +++ b/moldesign/_notebooks/.building/Header.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "![Molecular Design Toolkit](img/top.png)\n", + "![Molecular Design Toolkit](img/Top.png)\n", "\n", "[About](http://moldesign.bionano.autodesk.com/ \"MDT Website\")\n", "   [Tutorials](http://example.com/ \"Title\")\n", diff --git a/moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb b/moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb index a574823..e17d47c 100644 --- a/moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb +++ b/moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb @@ -7,7 +7,7 @@ "\n", "About      Forum      Issues      Tutorials      Documentation\n", "\n", - "![Molecular Design Toolkit](img/top.png)\n", + "![Molecular Design Toolkit](img/Top.png)\n", "
\n", "\n", "

Example 1: Build and simulate DNA

\n", diff --git a/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb b/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb index 7057e6c..16515fd 100644 --- a/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb +++ b/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb @@ -11,7 +11,7 @@ "Tutorials      \n", "Documentation\n", "\n", - "![Molecular Design Toolkit](img/top.png)\n", + "![Molecular Design Toolkit](img/Top.png)\n", "
\n", "

Example 2: Orbitals, Wavefunctions, and Potential Energy Surfaces

\n", "\n", diff --git a/moldesign/_notebooks/Getting Started.ipynb b/moldesign/_notebooks/Getting Started.ipynb index 3a05799..52f333a 100644 --- a/moldesign/_notebooks/Getting Started.ipynb +++ b/moldesign/_notebooks/Getting Started.ipynb @@ -6,7 +6,7 @@ "collapsed": true }, "source": [ - "![Molecular Design Toolkit](img/header.png)\n", + "![Molecular Design Toolkit](img/Header.png)\n", "\n", "
\n", "\n", @@ -67,7 +67,7 @@ "language_info": { "codemirror_mode": { "name": "ipython", - "version": 2 + "version": 2.0 }, "file_extension": ".py", "mimetype": "text/x-python", @@ -79,4 +79,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} +} \ No newline at end of file diff --git a/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb b/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb index 8e654b4..2f5ae80 100644 --- a/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb +++ b/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb @@ -7,7 +7,7 @@ "\n", "About      Forum      Issues      Tutorials      Documentation\n", "\n", - "![Molecular Design Toolkit](img/top.png)\n", + "![Molecular Design Toolkit](img/Top.png)\n", "
\n", "\n", "\n",