From d13debb42a6e7e6c4313b3f70755135d6d3184e9 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Mon, 1 May 2023 15:02:08 -0700
Subject: [PATCH 01/10] fix bash syntax issue
---
easyCampaign/cli-tutorial.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/easyCampaign/cli-tutorial.md b/easyCampaign/cli-tutorial.md
index 3110b44..2944def 100644
--- a/easyCampaign/cli-tutorial.md
+++ b/easyCampaign/cli-tutorial.md
@@ -96,7 +96,7 @@ like:
```
# this will take a long time!
-for file in transformations/*/*/*.json; do
+for file in transformations/**/*.json; do
relpath=${file:16} # strip off "transformations/"
dirpath=${relpath%.*} # strip off final ".json"
openfe quickrun $file -o results/$relpath -d results/$dirpath
@@ -112,7 +112,7 @@ computing center. Here is an example of a very simple script that will create
and submit a job script for the simplest SLURM use case:
```
-for file in transformations/*/*/*.json; do
+for file in transformations/**/*.json; do
relpath=${file:16} # strip off "transformations/"
dirpath=${relpath%.*} # strip off final ".json"
jobpath="transformations/${dirpath}.job"
From 9e217daf1e51b8479446692ebbc9fa1aa7775045 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Mon, 1 May 2023 15:59:47 -0700
Subject: [PATCH 02/10] start of notebook for CLI demo
---
easyCampaign/Cli Demo.ipynb | 50 +++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
create mode 100644 easyCampaign/Cli Demo.ipynb
diff --git a/easyCampaign/Cli Demo.ipynb b/easyCampaign/Cli Demo.ipynb
new file mode 100644
index 0000000..9ae16cc
--- /dev/null
+++ b/easyCampaign/Cli Demo.ipynb
@@ -0,0 +1,50 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "785f29f9-889f-43ea-93ed-824de546993b",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "!pip install -q condacolab\n",
+ "import condacolab\n",
+ "condacolab.install_from_url(https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2023/OpenFEforge-0.7.4-Linux-x86_64.sh)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c23f5c0d-a36e-43f5-9f1e-1e3f3fba80ea",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import condacolab\n",
+ "condacolab.check()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.10"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
From 589e3ec7b86a834e5eb15b4df5804cbc96ed1f75 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Mon, 1 May 2023 16:00:38 -0700
Subject: [PATCH 03/10] have nbval skip these cells
---
easyCampaign/Cli Demo.ipynb | 2 ++
1 file changed, 2 insertions(+)
diff --git a/easyCampaign/Cli Demo.ipynb b/easyCampaign/Cli Demo.ipynb
index 9ae16cc..08ba336 100644
--- a/easyCampaign/Cli Demo.ipynb
+++ b/easyCampaign/Cli Demo.ipynb
@@ -9,6 +9,7 @@
},
"outputs": [],
"source": [
+ "# NBVAL_SKIP\n",
"!pip install -q condacolab\n",
"import condacolab\n",
"condacolab.install_from_url(https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2023/OpenFEforge-0.7.4-Linux-x86_64.sh)"
@@ -21,6 +22,7 @@
"metadata": {},
"outputs": [],
"source": [
+ "# NBVAL_SKIP\n",
"import condacolab\n",
"condacolab.check()"
]
From d40569e65aa0826b8567f7060222a21e8b414a43 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Mon, 1 May 2023 16:03:04 -0700
Subject: [PATCH 04/10] fix syntax
---
easyCampaign/Cli Demo.ipynb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/easyCampaign/Cli Demo.ipynb b/easyCampaign/Cli Demo.ipynb
index 08ba336..c1d05a5 100644
--- a/easyCampaign/Cli Demo.ipynb
+++ b/easyCampaign/Cli Demo.ipynb
@@ -12,7 +12,7 @@
"# NBVAL_SKIP\n",
"!pip install -q condacolab\n",
"import condacolab\n",
- "condacolab.install_from_url(https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2023/OpenFEforge-0.7.4-Linux-x86_64.sh)"
+ "condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2023/OpenFEforge-0.7.4-Linux-x86_64.sh\")"
]
},
{
From 3972ed1773e11a9f11a33f0fdab0abb55ebfb01b Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Mon, 1 May 2023 16:21:13 -0700
Subject: [PATCH 05/10] This notebooks will give you a shell with openfe
---
easyCampaign/Cli Demo.ipynb | 57 +++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/easyCampaign/Cli Demo.ipynb b/easyCampaign/Cli Demo.ipynb
index c1d05a5..eaa5b6c 100644
--- a/easyCampaign/Cli Demo.ipynb
+++ b/easyCampaign/Cli Demo.ipynb
@@ -26,6 +26,63 @@
"import condacolab\n",
"condacolab.check()"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "4a9a49bd-4520-4ca6-96e1-378559248ac4",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# NBVAL_SKIP\n",
+ "from IPython.display import JSON\n",
+ "from google.colab import output\n",
+ "from subprocess import getoutput\n",
+ "import os\n",
+ "\n",
+ "def shell(command):\n",
+ " if command.startswith('cd'):\n",
+ " path = command.strip().split(maxsplit=1)[1]\n",
+ " os.chdir(path)\n",
+ " return JSON([''])\n",
+ " return JSON([getoutput(command)])\n",
+ "output.register_callback('shell', shell)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "cc0b6da8-b400-4795-8f31-10d00e941449",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# NBVAL_SKIP\n",
+ "#@title Colab Shell\n",
+ "%%html\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "