From 75e87b0ff2355e2e48aed881c0abdac298802867 Mon Sep 17 00:00:00 2001
From: kennykos <“gkosmacher01@gmail.com”>
Date: Thu, 9 Mar 2023 18:25:43 -0600
Subject: adding env file for binder

---
 environment.yml | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..f4334c3
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,9 @@
+name: toriis
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy=1.23.5 
+  - pandas=1.5.3
+  - requests=2.28.2
+  - yfinance=0.2.12=pyhd8ed1ab_0
-- 
cgit v1.2.3


From 800047ff43e3b351882b927bf671fdca3722bfac Mon Sep 17 00:00:00 2001
From: kennykos <“gkosmacher01@gmail.com”>
Date: Thu, 9 Mar 2023 18:32:04 -0600
Subject: added openpyxl dependency

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index f4334c3..9898f22 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,3 +7,4 @@ dependencies:
   - pandas=1.5.3
   - requests=2.28.2
   - yfinance=0.2.12=pyhd8ed1ab_0
+  - openpyxl=3.1.1
\ No newline at end of file
-- 
cgit v1.2.3


From 54759ff78f63bf62fc7c126dff64925d5c1fc105 Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Thu, 9 Mar 2023 18:41:59 -0600
Subject: Updating README with binder button and info

---
 README.md | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index e135132..8e19ed5 100644
--- a/README.md
+++ b/README.md
@@ -1,19 +1,28 @@
 # toriis-analysis
-Repository for scripts to evaluate public institutional investment data.
+Repository for scripts to evaluate public institutional investment data. These scripts are designed to be launched with [binder](https://mybinder.org/) so that other community members can run their own analyses without any additional setup.
+
+
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/toriis-portal/toriis-analysis/HEAD)
 
 # Running existing notebook
 
-1) 
-	+ Fork + clone repo
-	+ Run `setup/setup.sh` to set up the local conda environment
+1. **Interactive, UI-only:** Launch the repo in binder and clone one of the example notebooks
+1. **Interactive, CLI only:** 
+	1. Fork + clone repo
+	1. Run `setup/setup.sh` to set up the local conda environment
 		- you may need to install the correct version of miniconda
-	+ Start a local notebook suerver (`juypter notebook`)
+	1. Start a local notebook suerver (`juypter notebook`)
 
 # Contributing
 
 You are welcome to contribute data and analysis results. Please make sure that you contribute **cleared notebooks** so version control capabilities work well. To clear a notebook, use `Kernel -> Researt & Clear Output)` 
 
-1) **CLI:**
-	+ Create a new branch (`$ git checkout -b <branch_name>`)
-	+ Commit the new notebook/data (`$ git add <new file>; git commit`)
-	+ Push and generate a pull request
+1. **UI-only:**
+    1. Download the notebook (Download -> ipynb)
+    1. Upload the notebook using the GitHub UI (Upload Files, next to Clone or Download)
+1. **CLI only:** Follow the [instructions on github](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) - i.e.
+    1. Create a new branch (e.g. `$ git checkout -b`)
+    1. Commit the new notebook (e.g. `$ git add` and `$ git commit`)
+    1. Push and generate pull request 
+
-- 
cgit v1.2.3


From a7ebd83ba057d222d776afc9bd4a3ad252d51020 Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 11:16:46 -0600
Subject: Create analysis-notebook-test-binder.yml

Create a github action for binder tests based off
[https://github.com/MobilityNet/mobilitynet-analysis-scripts/blob/master/.github/workflows/exploratory-notebooks-test-binder.yml](https://github.com/MobilityNet/mobilitynet-analysis-scripts/blob/master/.github/workflows/exploratory-notebooks-test-binder.yml)
---
 .../workflows/analysis-notebook-test-binder.yml    | 120 +++++++++++++++++++++
 1 file changed, 120 insertions(+)
 create mode 100644 .github/workflows/analysis-notebook-test-binder.yml

diff --git a/.github/workflows/analysis-notebook-test-binder.yml b/.github/workflows/analysis-notebook-test-binder.yml
new file mode 100644
index 0000000..9269866
--- /dev/null
+++ b/.github/workflows/analysis-notebook-test-binder.yml
@@ -0,0 +1,120 @@
+# This is a basic workflow to help you get started with Actions
+
+name: analysis-notebook-test-binder
+
+# Controls when the action will run. Triggers the workflow on push or pull request 
+# events but only for the master branch
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron:  '5 4 * * 0'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # We would ideally have two jobs here called "build" and "test"
+  # However, in order to do that we would have to publish the image as an artifact
+  # to share it between jobs
+  # https://help.github.com/en/actions/configuring-and-managing-workflows/persisting-workflow-data-using-artifacts
+  # and it looks like the generated image is too large
+  # https://github.com/MobilityNet/mobilitynet-analysis-scripts/runs/613707818?check_suite_focus=true
+  # -rw-r--r-- 1 runner docker 3.3G Apr 23 21:37 /tmp/mobilitynet_84f67fcad71c.tar
+  # Filesystem      Size  Used Avail Use% Mounted on
+  # /dev/sda1        84G   79G  5.1G  94% /
+  # https://github.com/MobilityNet/mobilitynet-analysis-scripts/runs/612938777?check_suite_focus=true
+  # Fail to upload '/tmp/mobilitynet_ec3aba6d029f.tar' due to 'Blob is incomplete (missing block).
+  # while we figure out how to trim that, we have to run them as steps in the same job
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    outputs:
+        IMAGE_SHA_NAME: ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }}
+        OUT_IMGNAME: ${{ steps.package-build.outputs.OUT_IMGNAME }}
+    strategy:
+      matrix:
+        # Two tests are sufficient because the other notebooks are already
+        # tested in the manual install and the timeline notebooks are almost
+        # identical
+        target: [ui_security_inventory_23_parsing.ipynb]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Create a docker image using repo2docker
+      id: install-using-repo2docker
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        IMAGE_NAME: "toriis-analysis"
+
+    - name: Verify repo2docker environment
+      run: |
+        echo "image SHA was ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }}"
+        echo "Listing all images"
+        docker image list
+
+        echo "Checking to see if toriis-analysis exists"
+        docker image list | grep toriis-analysis | wc -l
+        echo "Checking to see if repo2docker creation image exists"
+        docker image list | grep repo2docker | wc -l
+
+        echo "Reading versions of related software"
+        echo "---- DOCKER ----"
+        docker --version
+        CURR_DOCKER_VER=`docker --version`
+        echo "---- CONDA ----"
+        docker run ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }} /srv/conda/bin/conda --version | cut -d " " -f 2
+        CURR_CONDA_VER=`docker run ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }} /srv/conda/bin/conda --version | cut -d " " -f 2`
+        echo "---- repo2docker----"
+        docker run jupyter/repo2docker:master pip3 list | grep jupyter-repo2docker
+        CURR_R2D_VER=`docker run jupyter/repo2docker:master pip3 list | grep jupyter-repo2docker`
+        echo "On checking, docker ver is $CURR_DOCKER_VER"
+        echo "             conda ver is $CURR_CONDA_VER and"
+        echo "             repo2docker ver is $CURR_R2D_VER"
+ 
+    - name: Start the recently built docker container
+      run: |
+        echo "image SHA was ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }}"
+        docker run --name toriis-analysis_test -d -p 8888:8888  ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }} jupyter notebook --ip 0.0.0.0
+
+    - name: Test the interactive timeline
+      run: |
+        echo "About to run notebooks"
+        docker exec toriis-analysis_test python bin/run_notebooks.py ${{ matrix.target }}
+        echo "After running the notebooks, checking container list"
+        docker container list
+
+    - name: Copy the failure output
+      id: copy-failure-output
+      if: failure()
+      run: |
+        OUT_FILENAME=`echo ${{ matrix.target }} | sed "s/.ipynb/_out.ipynb/"`
+        echo "output filename = $OUT_FILENAME"
+
+        echo "About to copy file from docker"
+        docker exec toriis-analysis_test ls
+        DOCKER_WD=`docker exec toriis-analysis_test pwd`
+        echo "DOCKER_WD=$DOCKER_WD"
+        docker exec toriis-analysis_test ls $DOCKER_WD
+        docker exec toriis-analysis_test ls $DOCKER_WD/$OUT_FILENAME
+        docker cp mobilitynet_test:$DOCKER_WD/$OUT_FILENAME /tmp
+        ls -al /tmp/$OUT_FILENAME
+        echo "::set-output name=OUT_FILENAME::${OUT_FILENAME}"
+
+    - name: Upload result for the interactive timeline
+      if: failure()
+      uses: actions/upload-artifact@v1
+      with:
+        name: ${{ steps.copy-failure-output.outputs.OUT_FILENAME }}
+        path: /tmp/${{ steps.copy-failure-output.outputs.OUT_FILENAME }}
+
+    - name: Shutdown the recently built docker container
+      run: |
+        echo "Running docker container list"
+        docker container list
+        docker stop mobilitynet_test
-- 
cgit v1.2.3


From 84e372d78cfe15f62f001e0ec7fa6409ce5d0c2e Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 11:19:41 -0600
Subject: Update analysis-notebook-test-binder.yml

changed workflow to test on branch 2-set-up-binder-1 for now, need to change back if the test passes
---
 .github/workflows/analysis-notebook-test-binder.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/analysis-notebook-test-binder.yml b/.github/workflows/analysis-notebook-test-binder.yml
index 9269866..f47a715 100644
--- a/.github/workflows/analysis-notebook-test-binder.yml
+++ b/.github/workflows/analysis-notebook-test-binder.yml
@@ -6,9 +6,9 @@ name: analysis-notebook-test-binder
 # events but only for the master branch
 on:
   push:
-    branches: [ main ]
+    branches: [ 2-set-up-binder-1 ]
   pull_request:
-    branches: [ main ]
+    branches: [ 2-set-up-binder-1 ]
   schedule:
     # * is a special character in YAML so you have to quote this string
     - cron:  '5 4 * * 0'
-- 
cgit v1.2.3


From d8d37232e3b8c7b10722438a8b8fbccf528a53e6 Mon Sep 17 00:00:00 2001
From: kennykos <“gkosmacher01@gmail.com”>
Date: Fri, 10 Mar 2023 11:35:53 -0600
Subject: updating env for setup

---
 setup/environment.yml   | 128 +++---------------------------------------------
 setup/setup.sh          |   2 +-
 setup/setup_conda.sh    |   2 +-
 setup/teardown.sh       |   2 +-
 setup/teardown_conda.sh |   2 +-
 5 files changed, 10 insertions(+), 126 deletions(-)

diff --git a/setup/environment.yml b/setup/environment.yml
index c72a998..9898f22 100644
--- a/setup/environment.yml
+++ b/setup/environment.yml
@@ -1,126 +1,10 @@
 name: toriis
 channels:
+  - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - anyio=3.5.0=py310h06a4308_0
-  - argon2-cffi=21.3.0=pyhd3eb1b0_0
-  - argon2-cffi-bindings=21.2.0=py310h7f8727e_0
-  - asttokens=2.0.5=pyhd3eb1b0_0
-  - attrs=22.1.0=py310h06a4308_0
-  - babel=2.11.0=py310h06a4308_0
-  - backcall=0.2.0=pyhd3eb1b0_0
-  - beautifulsoup4=4.11.1=py310h06a4308_0
-  - blas=1.0=mkl
-  - bleach=4.1.0=pyhd3eb1b0_0
-  - bottleneck=1.3.5=py310ha9d4c09_0
-  - brotlipy=0.7.0=py310h7f8727e_1002
-  - bzip2=1.0.8=h7b6447c_0
-  - ca-certificates=2023.01.10=h06a4308_0
-  - certifi=2022.12.7=py310h06a4308_0
-  - cffi=1.15.1=py310h5eee18b_3
-  - charset-normalizer=2.0.4=pyhd3eb1b0_0
-  - comm=0.1.2=py310h06a4308_0
-  - cryptography=38.0.4=py310h9ce1e76_0
-  - debugpy=1.5.1=py310h295c915_0
-  - decorator=5.1.1=pyhd3eb1b0_0
-  - defusedxml=0.7.1=pyhd3eb1b0_0
-  - entrypoints=0.4=py310h06a4308_0
-  - executing=0.8.3=pyhd3eb1b0_0
-  - flit-core=3.6.0=pyhd3eb1b0_0
-  - icu=58.2=he6710b0_3
-  - idna=3.4=py310h06a4308_0
-  - intel-openmp=2021.4.0=h06a4308_3561
-  - ipykernel=6.19.2=py310h2f386ee_0
-  - ipython=8.9.0=py310h06a4308_0
-  - ipython_genutils=0.2.0=pyhd3eb1b0_1
-  - jedi=0.18.1=py310h06a4308_1
-  - jinja2=3.1.2=py310h06a4308_0
-  - json5=0.9.6=pyhd3eb1b0_0
-  - jsonschema=4.16.0=py310h06a4308_0
-  - jupyter_client=7.4.9=py310h06a4308_0
-  - jupyter_core=5.1.1=py310h06a4308_0
-  - jupyter_server=1.23.4=py310h06a4308_0
-  - jupyterlab=3.5.3=py310h06a4308_0
-  - jupyterlab_pygments=0.1.2=py_0
-  - jupyterlab_server=2.16.5=py310h06a4308_0
-  - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.4.2=h6a678d5_6
-  - libgcc-ng=11.2.0=h1234567_1
-  - libgomp=11.2.0=h1234567_1
-  - libsodium=1.0.18=h7b6447c_0
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - libuuid=1.41.5=h5eee18b_0
-  - libxml2=2.9.14=h74e7548_0
-  - libxslt=1.1.35=h4e12654_0
-  - lxml=4.9.1=py310h1edc446_0
-  - markupsafe=2.1.1=py310h7f8727e_0
-  - matplotlib-inline=0.1.6=py310h06a4308_0
-  - mistune=0.8.4=py310h7f8727e_1000
-  - mkl=2021.4.0=h06a4308_640
-  - mkl-service=2.4.0=py310h7f8727e_0
-  - mkl_fft=1.3.1=py310hd6ae3a3_0
-  - mkl_random=1.2.2=py310h00e6091_0
-  - nbclassic=0.4.8=py310h06a4308_0
-  - nbclient=0.5.13=py310h06a4308_0
-  - nbconvert=6.5.4=py310h06a4308_0
-  - nbformat=5.7.0=py310h06a4308_0
-  - ncurses=6.4=h6a678d5_0
-  - nest-asyncio=1.5.6=py310h06a4308_0
-  - notebook=6.5.2=py310h06a4308_0
-  - notebook-shim=0.2.2=py310h06a4308_0
-  - numexpr=2.8.4=py310h8879344_0
-  - numpy=1.23.5=py310hd5efca6_0
-  - numpy-base=1.23.5=py310h8e6c178_0
-  - openssl=1.1.1t=h7f8727e_0
-  - packaging=22.0=py310h06a4308_0
-  - pandas=1.5.2=py310h1128e8f_0
-  - pandocfilters=1.5.0=pyhd3eb1b0_0
-  - parso=0.8.3=pyhd3eb1b0_0
-  - pexpect=4.8.0=pyhd3eb1b0_3
-  - pickleshare=0.7.5=pyhd3eb1b0_1003
-  - pip=22.3.1=py310h06a4308_0
-  - platformdirs=2.5.2=py310h06a4308_0
-  - prometheus_client=0.14.1=py310h06a4308_0
-  - prompt-toolkit=3.0.36=py310h06a4308_0
-  - psutil=5.9.0=py310h5eee18b_0
-  - ptyprocess=0.7.0=pyhd3eb1b0_2
-  - pure_eval=0.2.2=pyhd3eb1b0_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pygments=2.11.2=pyhd3eb1b0_0
-  - pyopenssl=22.0.0=pyhd3eb1b0_0
-  - pyrsistent=0.18.0=py310h7f8727e_0
-  - pysocks=1.7.1=py310h06a4308_0
-  - python=3.10.9=h7a1cb2a_0
-  - python-dateutil=2.8.2=pyhd3eb1b0_0
-  - python-fastjsonschema=2.16.2=py310h06a4308_0
-  - pytz=2022.7=py310h06a4308_0
-  - pyzmq=23.2.0=py310h6a678d5_0
-  - readline=8.2=h5eee18b_0
-  - requests=2.28.1=py310h06a4308_0
-  - send2trash=1.8.0=pyhd3eb1b0_1
-  - setuptools=65.6.3=py310h06a4308_0
-  - six=1.16.0=pyhd3eb1b0_1
-  - sniffio=1.2.0=py310h06a4308_1
-  - soupsieve=2.3.2.post1=py310h06a4308_0
-  - sqlite=3.40.1=h5082296_0
-  - stack_data=0.2.0=pyhd3eb1b0_0
-  - terminado=0.17.1=py310h06a4308_0
-  - tinycss2=1.2.1=py310h06a4308_0
-  - tk=8.6.12=h1ccaba5_0
-  - tomli=2.0.1=py310h06a4308_0
-  - tornado=6.2=py310h5eee18b_0
-  - traitlets=5.7.1=py310h06a4308_0
-  - typing-extensions=4.4.0=py310h06a4308_0
-  - typing_extensions=4.4.0=py310h06a4308_0
-  - tzdata=2022g=h04d1e81_0
-  - urllib3=1.26.14=py310h06a4308_0
-  - wcwidth=0.2.5=pyhd3eb1b0_0
-  - webencodings=0.5.1=py310h06a4308_1
-  - websocket-client=0.58.0=py310h06a4308_4
-  - wheel=0.37.1=pyhd3eb1b0_0
-  - xz=5.2.10=h5eee18b_1
-  - zeromq=4.3.4=h2531618_0
-  - zlib=1.2.13=h5eee18b_0
-prefix: /home/gabrielkosmacher/miniconda3/envs/toriis
+  - numpy=1.23.5 
+  - pandas=1.5.3
+  - requests=2.28.2
+  - yfinance=0.2.12=pyhd8ed1ab_0
+  - openpyxl=3.1.1
\ No newline at end of file
diff --git a/setup/setup.sh b/setup/setup.sh
index d2631f9..6730a4f 100644
--- a/setup/setup.sh
+++ b/setup/setup.sh
@@ -11,4 +11,4 @@ set -e
 source setup/checks/check_for_conda.sh
 
 conda env update --name toriis --file setup/environment.yml
-conda activate toriis
+conda activate toriis
\ No newline at end of file
diff --git a/setup/setup_conda.sh b/setup/setup_conda.sh
index e7d4e3e..ee4d57f 100644
--- a/setup/setup_conda.sh
+++ b/setup/setup_conda.sh
@@ -19,4 +19,4 @@ else
     # Useful for debugging any issues with conda
     conda info -a
     echo "Successfully installed at $INSTALL_PREFIX. Please run 'source $SOURCE_SCRIPT' in every terminal where you want to use conda"
-fi
+fi
\ No newline at end of file
diff --git a/setup/teardown.sh b/setup/teardown.sh
index 308fde8..f8ad631 100644
--- a/setup/teardown.sh
+++ b/setup/teardown.sh
@@ -1,3 +1,3 @@
 # taken from mobilitynet-analysis-scripts/setup/teardown.sh
 conda activate base
-conda env remove --name toriis
+conda env remove --name toriis
\ No newline at end of file
diff --git a/setup/teardown_conda.sh b/setup/teardown_conda.sh
index 2fde7a5..a61f834 100644
--- a/setup/teardown_conda.sh
+++ b/setup/teardown_conda.sh
@@ -6,4 +6,4 @@ if [ -z $EXP_CONDA_VER ]; then
 else
     INSTALL_PREFIX=$HOME/miniconda-$EXP_CONDA_VER
     rm -rf $INSTALL_PREFIX
-fi
+fi
\ No newline at end of file
-- 
cgit v1.2.3


From 4bf1a4d92776b9a72e42b22a3f7252abdd00c81d Mon Sep 17 00:00:00 2001
From: kennykos <“gkosmacher01@gmail.com”>
Date: Fri, 10 Mar 2023 11:36:13 -0600
Subject: updating directories to ignore

---
 .gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.gitignore b/.gitignore
index 76605c9..3ff48d8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,9 @@
 # Jupyter Notebook
 .ipynb_checkpoints
 
+# Directory's to ignore
+.conda
+.idea
+
 # Private Data
 data/FFIS-CU200-2021-Q4.xlsx
-- 
cgit v1.2.3


From f0def882f41f7ea9414203c0c16524104fd9e206 Mon Sep 17 00:00:00 2001
From: kennykos <“gkosmacher01@gmail.com”>
Date: Fri, 10 Mar 2023 12:12:23 -0600
Subject: adding script to bu used in the workflow

---
 bin/run_notebooks.py | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 bin/run_notebooks.py

diff --git a/bin/run_notebooks.py b/bin/run_notebooks.py
new file mode 100644
index 0000000..ea7e8ee
--- /dev/null
+++ b/bin/run_notebooks.py
@@ -0,0 +1,67 @@
+# ! python
+# coding: utf-8
+# From https://gist.github.com/tpogden/ec79f2ebe2baf45655445b575dc7f540
+# with some more context at https://ogden.eu/run-notebooks
+# Thanks to @tpogden for his gist
+
+import os
+import sys
+import argparse
+import glob
+
+import nbformat
+from nbconvert.preprocessors import ExecutePreprocessor
+from nbconvert.preprocessors.execute import CellExecutionError
+
+# Parse args
+parser = argparse.ArgumentParser(description="Runs a set of Jupyter \
+                                              notebooks.")
+file_text = """ Notebook file(s) to be run, e.g. '*.ipynb' (default),
+'my_nb1.ipynb', 'my_nb1.ipynb my_nb2.ipynb', 'my_dir/*.ipynb'
+"""
+parser.add_argument('file_list', metavar='F', type=str, nargs='*', 
+    help=file_text)
+parser.add_argument('-t', '--timeout', help='Length of time (in secs) a cell \
+    can run before raising TimeoutError (default 600).', default=600, 
+    required=False)
+parser.add_argument('-p', '--run-path', help='The path the notebook will be \
+    run from (default pwd).', default='.', required=False)
+args = parser.parse_args()
+print('Args:', args)
+if not args.file_list: # Default file_list
+    args.file_list = glob.glob('*.ipynb')
+
+# Check list of notebooks
+notebooks = []
+print('Notebooks to run:')
+for f in args.file_list:
+    # Find notebooks but not notebooks previously output from this script
+    if f.endswith('.ipynb') and not f.endswith('_out.ipynb'):
+        print(f[:-6])
+        notebooks.append(f[:-6]) # Want the filename without '.ipynb'
+
+# Execute notebooks and output
+num_notebooks = len(notebooks)
+print('*****')
+for i, n in enumerate(notebooks):
+    n_out = n + '_out'
+    with open(n + '.ipynb') as f:
+        nb = nbformat.read(f, as_version=4)
+        ep = ExecutePreprocessor(timeout=int(args.timeout), kernel_name='python3')
+        try:
+            print('Running', n, ':', i, '/', num_notebooks)
+            out = ep.preprocess(nb, {'metadata': {'path': args.run_path}})
+        except CellExecutionError:
+            out = None
+            msg = 'Error executing the notebook "%s".\n' % n
+            msg += 'See notebook "%s" for the traceback.' % n_out
+            print(msg)
+            sys.exit(1)
+        except TimeoutError:
+            msg = 'Timeout executing the notebook "%s".\n' % n
+            print(msg)
+            sys.exit(110)
+        finally:
+            # Write output file
+            with open(n_out + '.ipynb', mode='wt') as f:
+                nbformat.write(nb, f)
\ No newline at end of file
-- 
cgit v1.2.3


From 64cb5b512091d2c8cb956672b9706beeacc4797c Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 12:24:45 -0600
Subject: Update analysis-notebook-test-binder.yml

switched branches back to main, will open pr and debug in there.
---
 .github/workflows/analysis-notebook-test-binder.yml | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/analysis-notebook-test-binder.yml b/.github/workflows/analysis-notebook-test-binder.yml
index f47a715..b4e5469 100644
--- a/.github/workflows/analysis-notebook-test-binder.yml
+++ b/.github/workflows/analysis-notebook-test-binder.yml
@@ -3,30 +3,18 @@
 name: analysis-notebook-test-binder
 
 # Controls when the action will run. Triggers the workflow on push or pull request 
-# events but only for the master branch
+# events but only for the main branch
 on:
   push:
-    branches: [ 2-set-up-binder-1 ]
+    branches: [ main ]
   pull_request:
-    branches: [ 2-set-up-binder-1 ]
+    branches: [ main ]
   schedule:
     # * is a special character in YAML so you have to quote this string
     - cron:  '5 4 * * 0'
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # We would ideally have two jobs here called "build" and "test"
-  # However, in order to do that we would have to publish the image as an artifact
-  # to share it between jobs
-  # https://help.github.com/en/actions/configuring-and-managing-workflows/persisting-workflow-data-using-artifacts
-  # and it looks like the generated image is too large
-  # https://github.com/MobilityNet/mobilitynet-analysis-scripts/runs/613707818?check_suite_focus=true
-  # -rw-r--r-- 1 runner docker 3.3G Apr 23 21:37 /tmp/mobilitynet_84f67fcad71c.tar
-  # Filesystem      Size  Used Avail Use% Mounted on
-  # /dev/sda1        84G   79G  5.1G  94% /
-  # https://github.com/MobilityNet/mobilitynet-analysis-scripts/runs/612938777?check_suite_focus=true
-  # Fail to upload '/tmp/mobilitynet_ec3aba6d029f.tar' due to 'Blob is incomplete (missing block).
-  # while we figure out how to trim that, we have to run them as steps in the same job
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-- 
cgit v1.2.3


From 2d7b47b8f44b52d21e8df9ca1bce2c5cbd998944 Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 12:29:22 -0600
Subject: Update README.md

Added status badge
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 8e19ed5..c708323 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,4 @@
+[![analysis-notebook-test-binder](https://github.com/kennykos/toriis-analysis/actions/workflows/analysis-notebook-test-binder.yml/badge.svg)](https://github.com/kennykos/toriis-analysis/actions/workflows/analysis-notebook-test-binder.yml)
 # toriis-analysis
 Repository for scripts to evaluate public institutional investment data. These scripts are designed to be launched with [binder](https://mybinder.org/) so that other community members can run their own analyses without any additional setup.
 
-- 
cgit v1.2.3


From cbd3822d77c19f3cfb5b4595be9fa62e11839728 Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 12:53:15 -0600
Subject: Update analysis-notebook-test-binder.yml

change occurrences of mobilitynat to toriis-analysis
---
 .github/workflows/analysis-notebook-test-binder.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/analysis-notebook-test-binder.yml b/.github/workflows/analysis-notebook-test-binder.yml
index b4e5469..989fa65 100644
--- a/.github/workflows/analysis-notebook-test-binder.yml
+++ b/.github/workflows/analysis-notebook-test-binder.yml
@@ -90,7 +90,7 @@ jobs:
         echo "DOCKER_WD=$DOCKER_WD"
         docker exec toriis-analysis_test ls $DOCKER_WD
         docker exec toriis-analysis_test ls $DOCKER_WD/$OUT_FILENAME
-        docker cp mobilitynet_test:$DOCKER_WD/$OUT_FILENAME /tmp
+        docker cp toriis-analysis_test:$DOCKER_WD/$OUT_FILENAME /tmp
         ls -al /tmp/$OUT_FILENAME
         echo "::set-output name=OUT_FILENAME::${OUT_FILENAME}"
 
@@ -105,4 +105,4 @@ jobs:
       run: |
         echo "Running docker container list"
         docker container list
-        docker stop mobilitynet_test
+        docker stop toriis-analysis
-- 
cgit v1.2.3


From e747fe2a02de8277b626726c9e5afdc4acd6027a Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 13:05:21 -0600
Subject: Update analysis-notebook-test-binder.yml

changed toriis-analysis to toriis, I believe the - character was causing issues.
---
 .../workflows/analysis-notebook-test-binder.yml    | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/analysis-notebook-test-binder.yml b/.github/workflows/analysis-notebook-test-binder.yml
index 989fa65..c2c2dc7 100644
--- a/.github/workflows/analysis-notebook-test-binder.yml
+++ b/.github/workflows/analysis-notebook-test-binder.yml
@@ -38,7 +38,7 @@ jobs:
       id: install-using-repo2docker
       uses: jupyterhub/repo2docker-action@master
       with:
-        IMAGE_NAME: "toriis-analysis"
+        IMAGE_NAME: "toriis"
 
     - name: Verify repo2docker environment
       run: |
@@ -46,8 +46,8 @@ jobs:
         echo "Listing all images"
         docker image list
 
-        echo "Checking to see if toriis-analysis exists"
-        docker image list | grep toriis-analysis | wc -l
+        echo "Checking to see if toriis exists"
+        docker image list | grep toriis | wc -l
         echo "Checking to see if repo2docker creation image exists"
         docker image list | grep repo2docker | wc -l
 
@@ -68,12 +68,12 @@ jobs:
     - name: Start the recently built docker container
       run: |
         echo "image SHA was ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }}"
-        docker run --name toriis-analysis_test -d -p 8888:8888  ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }} jupyter notebook --ip 0.0.0.0
+        docker run --name toriis_test -d -p 8888:8888  ${{ steps.install-using-repo2docker.outputs.IMAGE_SHA_NAME }} jupyter notebook --ip 0.0.0.0
 
     - name: Test the interactive timeline
       run: |
         echo "About to run notebooks"
-        docker exec toriis-analysis_test python bin/run_notebooks.py ${{ matrix.target }}
+        docker exec toriis_test python bin/run_notebooks.py ${{ matrix.target }}
         echo "After running the notebooks, checking container list"
         docker container list
 
@@ -85,12 +85,12 @@ jobs:
         echo "output filename = $OUT_FILENAME"
 
         echo "About to copy file from docker"
-        docker exec toriis-analysis_test ls
-        DOCKER_WD=`docker exec toriis-analysis_test pwd`
+        docker exec toriis_test ls
+        DOCKER_WD=`docker exec toriis_test pwd`
         echo "DOCKER_WD=$DOCKER_WD"
-        docker exec toriis-analysis_test ls $DOCKER_WD
-        docker exec toriis-analysis_test ls $DOCKER_WD/$OUT_FILENAME
-        docker cp toriis-analysis_test:$DOCKER_WD/$OUT_FILENAME /tmp
+        docker exec toriis_test ls $DOCKER_WD
+        docker exec toriis_test ls $DOCKER_WD/$OUT_FILENAME
+        docker cp toriis_test:$DOCKER_WD/$OUT_FILENAME /tmp
         ls -al /tmp/$OUT_FILENAME
         echo "::set-output name=OUT_FILENAME::${OUT_FILENAME}"
 
@@ -105,4 +105,4 @@ jobs:
       run: |
         echo "Running docker container list"
         docker container list
-        docker stop toriis-analysis
+        docker stop toriis
-- 
cgit v1.2.3


From 85b7be2354de05b877ba54d84b2c6845cf337902 Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 13:15:19 -0600
Subject: Update analysis-notebook-test-binder.yml

---
 .github/workflows/analysis-notebook-test-binder.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/analysis-notebook-test-binder.yml b/.github/workflows/analysis-notebook-test-binder.yml
index c2c2dc7..e0185c0 100644
--- a/.github/workflows/analysis-notebook-test-binder.yml
+++ b/.github/workflows/analysis-notebook-test-binder.yml
@@ -36,7 +36,7 @@ jobs:
 
     - name: Create a docker image using repo2docker
       id: install-using-repo2docker
-      uses: jupyterhub/repo2docker-action@master
+      uses: shankari/repo2docker-action@master
       with:
         IMAGE_NAME: "toriis"
 
-- 
cgit v1.2.3


From d92093d87deee8b0a03a13af4a53f78753e9ab77 Mon Sep 17 00:00:00 2001
From: Gabriel Kosmacher <73120774+kennykos@users.noreply.github.com>
Date: Fri, 10 Mar 2023 13:45:53 -0600
Subject: Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index c708323..56e51d9 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-[![analysis-notebook-test-binder](https://github.com/kennykos/toriis-analysis/actions/workflows/analysis-notebook-test-binder.yml/badge.svg)](https://github.com/kennykos/toriis-analysis/actions/workflows/analysis-notebook-test-binder.yml)
+[![analysis-notebook-test-binder](https://github.com/toriis-portal/toriis-analysis/actions/workflows/analysis-notebook-test-binder.yml/badge.svg)](https://github.com/toriis-portal/toriis-analysis/actions/workflows/analysis-notebook-test-binder.yml)
 # toriis-analysis
 Repository for scripts to evaluate public institutional investment data. These scripts are designed to be launched with [binder](https://mybinder.org/) so that other community members can run their own analyses without any additional setup.
 
-- 
cgit v1.2.3