From ff6320807a3012750b0989a44869fb7557001b37 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Wed, 15 Nov 2023 16:16:09 -0500
Subject: [PATCH] Add source-related files for Synapse 3.1.1

---
 synapse/3.1.1/.gitignore      |  1 +
 synapse/3.1.1/README.md       | 68 +++++++++++++++++++++++++++++++++++
 synapse/3.1.1/environment.yml | 12 +++++++
 3 files changed, 81 insertions(+)
 create mode 100755 synapse/3.1.1/.gitignore
 create mode 100755 synapse/3.1.1/README.md
 create mode 100755 synapse/3.1.1/environment.yml

diff --git a/synapse/3.1.1/.gitignore b/synapse/3.1.1/.gitignore
new file mode 100755
index 0000000..3212987
--- /dev/null
+++ b/synapse/3.1.1/.gitignore
@@ -0,0 +1 @@
+synapse_env
diff --git a/synapse/3.1.1/README.md b/synapse/3.1.1/README.md
new file mode 100755
index 0000000..23c6ba5
--- /dev/null
+++ b/synapse/3.1.1/README.md
@@ -0,0 +1,68 @@
+# Installation
+
+```bash
+## Commands used for installing the software
+
+#   Make sure not to rely on user packages
+export PYTHONNOUSERSITE="anything"
+
+#   Create an 'environment.yml' file describing the conda environment we'll
+#   create
+echo "channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python = 3.10.4
+  - pip
+  - pip:
+      - synapseclient == 3.1.1
+      - pandas
+      - pysftp
+      - pyyaml
+      - pyhere" > environment.yml
+
+#   Create a conda environment containing the python-based and command-line-
+#   based synapse client
+module load conda/3-23.3.1
+conda env create -f environment.yml -p $PWD/synapse_env
+
+## Ignore all downloaded/installed files
+echo "synapse_env" > .gitignore
+
+#  Allow fairly relaxed permissions, but protect against accidental changes to
+#  the conda environment
+chmod -R 775 .
+chmod -R 555 synapse_env
+
+## Version control files
+git add .gitignore
+git add README.md
+git add environment.yml
+```
+
+# Reproducibility
+
+```bash
+## Evaluate the following commands
+module list
+date
+echo "User: ${USER}"
+echo "Node name: ${SLURMD_NODENAME}"
+```
+
+```bash
+## copy paste the output from the previous commands
+$ module list
+
+Currently Loaded Modules:
+  1) JHPCE_ROCKY9_DEFAULT_ENV   2) JHPCE_tools/3.0   3) conda/3-23.3.1
+
+ 
+
+$ date
+Wed Nov 15 04:15:19 PM EST 2023
+$ echo "User: ${USER}"
+User: neagles
+$ echo "Node name: ${SLURMD_NODENAME}"
+Node name: compute-114
+```
diff --git a/synapse/3.1.1/environment.yml b/synapse/3.1.1/environment.yml
new file mode 100755
index 0000000..c609f5a
--- /dev/null
+++ b/synapse/3.1.1/environment.yml
@@ -0,0 +1,12 @@
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python = 3.10.4
+  - pip
+  - pip:
+      - synapseclient == 3.1.1
+      - pandas
+      - pysftp
+      - pyyaml
+      - pyhere