From 796e7d66ea02912aca1e50ffea8062ca692e836e Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 15:52:20 -0500
Subject: [PATCH 01/39] Comment out line

---
 .github/workflows/create_test_conda_env.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create_test_conda_env.yml b/.github/workflows/create_test_conda_env.yml
index d04398bd..fee9c9aa 100644
--- a/.github/workflows/create_test_conda_env.yml
+++ b/.github/workflows/create_test_conda_env.yml
@@ -72,7 +72,7 @@ jobs:
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.ref == 'refs/heads/main' }}
+#        if: ${{ github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}

From 215332c4a1fe4c42d1b51aebe63717f0084c3098 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 15:55:20 -0500
Subject: [PATCH 02/39] small, trivial commit

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

diff --git a/fre/README.md b/fre/README.md
index 4570b317..27a0dfbd 100644
--- a/fre/README.md
+++ b/fre/README.md
@@ -16,7 +16,7 @@ The [tool group] fre-cli tools are described below ([Subcommands](#subcommands))
 ## **Usage (Users)**
 -->
 * Refer to fre-cli [README.md](https://github.com/NOAA-GFDL/fre-cli/blob/main/README.md) for usage and tips.
-
+hi
 <!--
 * [tool group] package repository located at: _insert permalink_
 

From 17ce7bfdaf6ac3078ecaac2f495cc013215adae4 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 15:56:56 -0500
Subject: [PATCH 03/39] Just working on docs

---
 .github/workflows/create_test_conda_env.yml | 60 ++++++++++-----------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/create_test_conda_env.yml b/.github/workflows/create_test_conda_env.yml
index fee9c9aa..908331f8 100644
--- a/.github/workflows/create_test_conda_env.yml
+++ b/.github/workflows/create_test_conda_env.yml
@@ -32,36 +32,36 @@ jobs:
           ## called as a module (-m pip) for explicitness
           $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .
 
-      - name: Run pytest in fre-cli environment
-        run: |
-          # try to make sure the right things are in GITHUB_PATH
-          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-          
-          # are we talking to the right python?
-          which python
-          python --version
-          $CONDA/envs/fre-cli/bin/python --version
-          
-          # run pytest
-          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
-          
-          # install genbadge to generate coverage badge based on xml
-          pip install genbadge
-          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg
-          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg
-        
-      - name: Run pylint in fre-cli environment
-        run: |
-          # try to make sure the right things are in GITHUB_PATH
-          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-
-          # are we talking to the right python?
-          which python
-          python --version
-          $CONDA/envs/fre-cli/bin/python --version
-          
-          # run pylint, ignored modules avoid warnings arising from code internal to those modules 
-          pylint --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."
+#      - name: Run pytest in fre-cli environment
+#        run: |
+#          # try to make sure the right things are in GITHUB_PATH
+#          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
+#          
+#          # are we talking to the right python?
+#          which python
+#          python --version
+#          $CONDA/envs/fre-cli/bin/python --version
+#          
+#          # run pytest
+#          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
+#          
+#          # install genbadge to generate coverage badge based on xml
+#          pip install genbadge
+#          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg
+#          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg
+#        
+#      - name: Run pylint in fre-cli environment
+#        run: |
+#          # try to make sure the right things are in GITHUB_PATH
+#          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
+#
+#          # are we talking to the right python?
+#          which python
+#          python --version
+#          $CONDA/envs/fre-cli/bin/python --version
+#          
+#          # run pylint, ignored modules avoid warnings arising from code internal to those modules 
+#          pylint --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."
 
       - name: Install Sphinx and Build Documentation
         run: |

From 664c8ff1c172f2e83002e418835f3674203f089f Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:00:55 -0500
Subject: [PATCH 04/39] Remove hi

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

diff --git a/fre/README.md b/fre/README.md
index 27a0dfbd..61fe14d0 100644
--- a/fre/README.md
+++ b/fre/README.md
@@ -16,7 +16,7 @@ The [tool group] fre-cli tools are described below ([Subcommands](#subcommands))
 ## **Usage (Users)**
 -->
 * Refer to fre-cli [README.md](https://github.com/NOAA-GFDL/fre-cli/blob/main/README.md) for usage and tips.
-hi
+  
 <!--
 * [tool group] package repository located at: _insert permalink_
 

From 0ca5a70cae91ae982d8a81ad00d7eac6f890c864 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:10:58 -0500
Subject: [PATCH 05/39] Update README.md

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

diff --git a/fre/README.md b/fre/README.md
index 61fe14d0..e02112fd 100644
--- a/fre/README.md
+++ b/fre/README.md
@@ -16,7 +16,7 @@ The [tool group] fre-cli tools are described below ([Subcommands](#subcommands))
 ## **Usage (Users)**
 -->
 * Refer to fre-cli [README.md](https://github.com/NOAA-GFDL/fre-cli/blob/main/README.md) for usage and tips.
-  
+  hi
 <!--
 * [tool group] package repository located at: _insert permalink_
 

From 7959d4705fa99ed756d7e187a5e7b317d2e6242e Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:12:46 -0500
Subject: [PATCH 06/39] Update README.md

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

diff --git a/fre/README.md b/fre/README.md
index e02112fd..4570b317 100644
--- a/fre/README.md
+++ b/fre/README.md
@@ -16,7 +16,7 @@ The [tool group] fre-cli tools are described below ([Subcommands](#subcommands))
 ## **Usage (Users)**
 -->
 * Refer to fre-cli [README.md](https://github.com/NOAA-GFDL/fre-cli/blob/main/README.md) for usage and tips.
-  hi
+
 <!--
 * [tool group] package repository located at: _insert permalink_
 

From 42de8a121e98f705417e5569438bd22f9e7bc17c Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:14:48 -0500
Subject: [PATCH 07/39] Update README.md

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

diff --git a/fre/README.md b/fre/README.md
index 4570b317..5a1fc7f5 100644
--- a/fre/README.md
+++ b/fre/README.md
@@ -16,7 +16,7 @@ The [tool group] fre-cli tools are described below ([Subcommands](#subcommands))
 ## **Usage (Users)**
 -->
 * Refer to fre-cli [README.md](https://github.com/NOAA-GFDL/fre-cli/blob/main/README.md) for usage and tips.
-
+ah
 <!--
 * [tool group] package repository located at: _insert permalink_
 

From 5be56c35f2ba74ff5b2467254dc14194d77dd674 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:16:43 -0500
Subject: [PATCH 08/39] Update README.md

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

diff --git a/fre/README.md b/fre/README.md
index 5a1fc7f5..4570b317 100644
--- a/fre/README.md
+++ b/fre/README.md
@@ -16,7 +16,7 @@ The [tool group] fre-cli tools are described below ([Subcommands](#subcommands))
 ## **Usage (Users)**
 -->
 * Refer to fre-cli [README.md](https://github.com/NOAA-GFDL/fre-cli/blob/main/README.md) for usage and tips.
-ah
+
 <!--
 * [tool group] package repository located at: _insert permalink_
 

From a4bddaec7df4e58438be4dd2a487caaa802ada42 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:49:49 -0500
Subject: [PATCH 09/39] Create OWN-create_test_conda_env.yml

---
 .../workflows/OWN-create_test_conda_env.yml   | 80 +++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 .github/workflows/OWN-create_test_conda_env.yml

diff --git a/.github/workflows/OWN-create_test_conda_env.yml b/.github/workflows/OWN-create_test_conda_env.yml
new file mode 100644
index 00000000..908331f8
--- /dev/null
+++ b/.github/workflows/OWN-create_test_conda_env.yml
@@ -0,0 +1,80 @@
+name: create_test_conda_env
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '>=3.9'
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an env var pointing to root of miniconda dir
+          echo $CONDA/bin >> $GITHUB_PATH
+
+      - name: Create fre-cli environment
+        run: |
+          # create environment containing all dependencies
+          # the env cannot be explicitly activated in github CI/CD
+          conda env create -f environment.yml --name fre-cli
+
+          # add conda env's executables to github's PATH equiv.
+          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
+
+          ## use *conda environment's pip* to install fre-cli
+          ## called w/ full path to conda's python for explicitness
+          ## called as a module (-m pip) for explicitness
+          $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .
+
+#      - name: Run pytest in fre-cli environment
+#        run: |
+#          # try to make sure the right things are in GITHUB_PATH
+#          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
+#          
+#          # are we talking to the right python?
+#          which python
+#          python --version
+#          $CONDA/envs/fre-cli/bin/python --version
+#          
+#          # run pytest
+#          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
+#          
+#          # install genbadge to generate coverage badge based on xml
+#          pip install genbadge
+#          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg
+#          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg
+#        
+#      - name: Run pylint in fre-cli environment
+#        run: |
+#          # try to make sure the right things are in GITHUB_PATH
+#          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
+#
+#          # are we talking to the right python?
+#          which python
+#          python --version
+#          $CONDA/envs/fre-cli/bin/python --version
+#          
+#          # run pylint, ignored modules avoid warnings arising from code internal to those modules 
+#          pylint --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."
+
+      - name: Install Sphinx and Build Documentation
+        run: |
+          pip install sphinx renku-sphinx-theme sphinx-rtd-theme          
+          pip install --upgrade sphinx-rtd-theme
+          sphinx-apidoc --output-dir docs fre/ --separate
+          sphinx-build docs build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+#        if: ${{ github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: build/
+          force_orphan: true

From d49fd6a30b46e6ca0962732c1361e35249e3bea0 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 16:53:55 -0500
Subject: [PATCH 10/39] Add fre make doc to usage.rst

---
 docs/usage.rst | 123 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 122 insertions(+), 1 deletion(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index bd7ee348..648a894a 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -46,7 +46,128 @@ Brief rundown of commands also provided below:
 ============
 
 .. include:: fre_make.rst
-  
+
+1. create-checkuot
+2. create-makefile
+3. create-compile
+4. create-dockerfile
+5. run-fremake
+
+**Quickstart**
+
+#. **Bare-metal Build:**
+
+.. codeblock:: bash
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create and run the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
+
+#. **Bare-metal Build Multi-target:**
+
+.. codeblock:: bash
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create and run the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
+
+#. **Container Build:**
+
+In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
+
+.. codeblock:: bash
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p hpcme.2023 -t prod
+
+  # Create Dockerfile
+  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod
+
+  # Create and run the Dockerfile
+  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
+
+#. **Run all of fremake:**
+
+.. codeblock:: bash
+
+  # Bare-metal
+  fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Container
+  fre make run-fremake -y am5.yaml -p hpcme.2023 -t prod -npc
+
+#. **Bare-metal Build:**
+
+.. codeblock:: bash
+
+  # Create checkout script
+  fre make create-checkout -y [model yaml file] -p [platform] -t [target]
+
+  # Create and run checkout script
+  fre make create-checkout -y [model yaml file] -p [platform] -t [target] --execute
+
+  # Create Makefile
+  fre make create-makefile -y [model yaml file] -p [platform] -t [target]
+
+  # Creat the compile script
+  fre make create-compile -y [model yaml file] -p [platform] -t [target]
+
+  # Create and run the compile script
+  fre make create-compile -y [model yaml file] -p [platform] -t [target] --execute
+
+  # Run all of fremake
+  fre make run-fremake -y [model yaml file] -p [platform] -t [target] [other options...]
+
+#. **Container Build:**
+
+For the container build, parallel checkouts are not supported, so the `-npc` options must be used for the checkout script. In addition the platform must be a container platform.
+
+***To reiterate, users will not be able to create containers unless they have podman access on gaea.***
+
+.. codeblock:: bash
+
+  # Create checkout script
+  fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] -npc
+
+  # Create and run checkout script
+  fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
+
+  # Create Makefile
+  fre make create-makefile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target]
+
+  # Create a Dockerfile
+  fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target]
+
+  # Create and run the Dockerfile
+  fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
 
 ``fre pp``
 ==========

From 85a4ec2b2c9318d4562de50129e84f34974153b6 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:04:35 -0500
Subject: [PATCH 11/39] Update code block

---
 docs/usage.rst | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index 648a894a..ec2591a4 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -55,7 +55,7 @@ Brief rundown of commands also provided below:
 
 **Quickstart**
 
-#. **Bare-metal Build:**
+1. **Bare-metal Build:**
 
 .. codeblock:: bash
 
@@ -74,7 +74,7 @@ Brief rundown of commands also provided below:
   # Create and run the compile script
   fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
 
-#. **Bare-metal Build Multi-target:**
+2. **Bare-metal Build Multi-target:**
 
 .. codeblock:: bash
 
@@ -93,7 +93,7 @@ Brief rundown of commands also provided below:
   # Create and run the compile script
   fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
 
-#. **Container Build:**
+3. **Container Build:**
 
 In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
 
@@ -114,9 +114,9 @@ In order for the container to build successfully, a `-npc`, or `--no-parallel-ch
   # Create and run the Dockerfile
   fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
 
-#. **Run all of fremake:**
+4. **Run all of fremake:**
 
-.. codeblock:: bash
+.. codeblock:: 
 
   # Bare-metal
   fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
@@ -124,9 +124,11 @@ In order for the container to build successfully, a `-npc`, or `--no-parallel-ch
   # Container
   fre make run-fremake -y am5.yaml -p hpcme.2023 -t prod -npc
 
+**Guide**
+
 #. **Bare-metal Build:**
 
-.. codeblock:: bash
+.. codeblock:: 
 
   # Create checkout script
   fre make create-checkout -y [model yaml file] -p [platform] -t [target]
@@ -152,7 +154,7 @@ For the container build, parallel checkouts are not supported, so the `-npc` opt
 
 ***To reiterate, users will not be able to create containers unless they have podman access on gaea.***
 
-.. codeblock:: bash
+.. codeblock:: 
 
   # Create checkout script
   fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] -npc

From cbb00f5bd95a0aeb49c4268eb3ac8859f26fb0df Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:07:34 -0500
Subject: [PATCH 12/39] Update OWN-create_test_conda_env.yml

---
 .github/workflows/OWN-create_test_conda_env.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/OWN-create_test_conda_env.yml b/.github/workflows/OWN-create_test_conda_env.yml
index 908331f8..f2d29514 100644
--- a/.github/workflows/OWN-create_test_conda_env.yml
+++ b/.github/workflows/OWN-create_test_conda_env.yml
@@ -72,7 +72,7 @@ jobs:
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
-#        if: ${{ github.ref == 'refs/heads/main' }}
+        if: ${{ github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}

From ff6f86253e9e1b76d714e2774f4e0b7dfe48a410 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:08:39 -0500
Subject: [PATCH 13/39] Update OWN-create_test_conda_env.yml

---
 .github/workflows/OWN-create_test_conda_env.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/OWN-create_test_conda_env.yml b/.github/workflows/OWN-create_test_conda_env.yml
index f2d29514..8bca3b66 100644
--- a/.github/workflows/OWN-create_test_conda_env.yml
+++ b/.github/workflows/OWN-create_test_conda_env.yml
@@ -1,4 +1,4 @@
-name: create_test_conda_env
+name: own_create_test_conda_env
 
 on: [push]
 

From 3f52469364d958451fbeb89ccf05ab861fcb809f Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:14:14 -0500
Subject: [PATCH 14/39] Fix code-blocks

---
 docs/usage.rst | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index ec2591a4..b555d54b 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -57,7 +57,7 @@ Brief rundown of commands also provided below:
 
 1. **Bare-metal Build:**
 
-.. codeblock:: bash
+.. code-block:: 
 
   # Create checkout script
   fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod
@@ -76,7 +76,7 @@ Brief rundown of commands also provided below:
 
 2. **Bare-metal Build Multi-target:**
 
-.. codeblock:: bash
+.. code-block:: 
 
   # Create checkout script
   fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug
@@ -97,7 +97,7 @@ Brief rundown of commands also provided below:
 
 In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
 
-.. codeblock:: bash
+.. code-block:: 
 
   # Create checkout script
   fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc
@@ -116,7 +116,7 @@ In order for the container to build successfully, a `-npc`, or `--no-parallel-ch
 
 4. **Run all of fremake:**
 
-.. codeblock:: 
+.. code-block:: 
 
   # Bare-metal
   fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
@@ -126,9 +126,9 @@ In order for the container to build successfully, a `-npc`, or `--no-parallel-ch
 
 **Guide**
 
-#. **Bare-metal Build:**
+1. **Bare-metal Build:**
 
-.. codeblock:: 
+.. code-block:: 
 
   # Create checkout script
   fre make create-checkout -y [model yaml file] -p [platform] -t [target]
@@ -148,13 +148,13 @@ In order for the container to build successfully, a `-npc`, or `--no-parallel-ch
   # Run all of fremake
   fre make run-fremake -y [model yaml file] -p [platform] -t [target] [other options...]
 
-#. **Container Build:**
+2. **Container Build:**
 
 For the container build, parallel checkouts are not supported, so the `-npc` options must be used for the checkout script. In addition the platform must be a container platform.
 
 ***To reiterate, users will not be able to create containers unless they have podman access on gaea.***
 
-.. codeblock:: 
+.. code-block:: 
 
   # Create checkout script
   fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] -npc

From 265d25e50029c23b36420f2dbabac613b89cdc8b Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:15:39 -0500
Subject: [PATCH 15/39] Update publish_conda.yml

---
 .github/workflows/publish_conda.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/publish_conda.yml b/.github/workflows/publish_conda.yml
index b7a20fd8..ed9f4fd9 100644
--- a/.github/workflows/publish_conda.yml
+++ b/.github/workflows/publish_conda.yml
@@ -13,11 +13,11 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: 'recursive'
-      - name: Run Conda to Build and Publish
-        run: |
-          conda config --append channels conda-forge
-          conda config --append channels noaa-gfdl
-          conda install conda-build anaconda-client conda-verify
-          export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
-          conda config --set anaconda_upload yes
-          conda build .
+#      - name: Run Conda to Build and Publish
+#        run: |
+#          conda config --append channels conda-forge
+#          conda config --append channels noaa-gfdl
+#          conda install conda-build anaconda-client conda-verify
+#          export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
+#          conda config --set anaconda_upload yes
+#          conda build .

From 7ab9e10b1d93b9dfd84c6e40cbeeb9007347a53f Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:19:26 -0500
Subject: [PATCH 16/39] Update create_test_conda_env.yml

---
 .github/workflows/create_test_conda_env.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create_test_conda_env.yml b/.github/workflows/create_test_conda_env.yml
index 908331f8..f2d29514 100644
--- a/.github/workflows/create_test_conda_env.yml
+++ b/.github/workflows/create_test_conda_env.yml
@@ -72,7 +72,7 @@ jobs:
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
-#        if: ${{ github.ref == 'refs/heads/main' }}
+        if: ${{ github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}

From b5d00bbb939f826b594bd8e818297a769d6ed305 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:20:18 -0500
Subject: [PATCH 17/39] Delete .github/workflows/OWN-create_test_conda_env.yml

---
 .../workflows/OWN-create_test_conda_env.yml   | 80 -------------------
 1 file changed, 80 deletions(-)
 delete mode 100644 .github/workflows/OWN-create_test_conda_env.yml

diff --git a/.github/workflows/OWN-create_test_conda_env.yml b/.github/workflows/OWN-create_test_conda_env.yml
deleted file mode 100644
index 8bca3b66..00000000
--- a/.github/workflows/OWN-create_test_conda_env.yml
+++ /dev/null
@@ -1,80 +0,0 @@
-name: own_create_test_conda_env
-
-on: [push]
-
-jobs:
-  build-linux:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '>=3.9'
-      - name: Add conda to system path
-        run: |
-          # $CONDA is an env var pointing to root of miniconda dir
-          echo $CONDA/bin >> $GITHUB_PATH
-
-      - name: Create fre-cli environment
-        run: |
-          # create environment containing all dependencies
-          # the env cannot be explicitly activated in github CI/CD
-          conda env create -f environment.yml --name fre-cli
-
-          # add conda env's executables to github's PATH equiv.
-          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-
-          ## use *conda environment's pip* to install fre-cli
-          ## called w/ full path to conda's python for explicitness
-          ## called as a module (-m pip) for explicitness
-          $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .
-
-#      - name: Run pytest in fre-cli environment
-#        run: |
-#          # try to make sure the right things are in GITHUB_PATH
-#          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-#          
-#          # are we talking to the right python?
-#          which python
-#          python --version
-#          $CONDA/envs/fre-cli/bin/python --version
-#          
-#          # run pytest
-#          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
-#          
-#          # install genbadge to generate coverage badge based on xml
-#          pip install genbadge
-#          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg
-#          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg
-#        
-#      - name: Run pylint in fre-cli environment
-#        run: |
-#          # try to make sure the right things are in GITHUB_PATH
-#          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-#
-#          # are we talking to the right python?
-#          which python
-#          python --version
-#          $CONDA/envs/fre-cli/bin/python --version
-#          
-#          # run pylint, ignored modules avoid warnings arising from code internal to those modules 
-#          pylint --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."
-
-      - name: Install Sphinx and Build Documentation
-        run: |
-          pip install sphinx renku-sphinx-theme sphinx-rtd-theme          
-          pip install --upgrade sphinx-rtd-theme
-          sphinx-apidoc --output-dir docs fre/ --separate
-          sphinx-build docs build
-
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.ref == 'refs/heads/main' }}
-        with:
-          publish_branch: gh-pages
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: build/
-          force_orphan: true

From 5bc7aa50c458b34c730a11cec0b73881ae31106f Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:22:49 -0500
Subject: [PATCH 18/39] Add fre make subtools

---
 docs/usage.rst | 67 ++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 60 insertions(+), 7 deletions(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index b555d54b..136ae989 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -45,13 +45,66 @@ Brief rundown of commands also provided below:
 ``fre make``
 ============
 
-.. include:: fre_make.rst
-
-1. create-checkuot
-2. create-makefile
-3. create-compile
-4. create-dockerfile
-5. run-fremake
+Through the fre-cli, `fre make` can be used to create and run a checkout script, makefile, and compile a model.
+
+* Fremake Canopy Supports:
+   - multiple targets; use `-t` flag to define each target
+   - bare-metal build
+   - container creation
+   - parallel checkouts for bare-metal build**
+
+** **Note: Users will not be able to create containers without access to podman**
+
+The fremake canopy fre-cli subcommands are described below ([Subtools](#subtools)), as well as a Guide on the order in which to use them ([Guide](#guide)).
+
+Additionally, as mentioned, multiple targets can be used more multiple target-platform combinations.
+
+**Subtools**
+
+- `fre make create-checkout [options]`
+   - Purpose: Creates the checkout script and can check out source code (with execute option)
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+        - `-j, --jobs [number of jobs to run simultneously]`
+        - `-npc, --no-parallel-checkout (for container build)`
+        - `-e, --execute`
+
+- `fre make create-makefile [options]`
+   - Purpose: Creates the makefile
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+
+- `fre make create-compile [options]`
+   - Purpose: Creates the compile script and compiles the model (with execute option)
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+        - `-j, --jobs [number of jobs to run simultneously]`
+        - `-n, --parallel [number of concurrent modile compiles]`
+        - `-e, --execute`
+
+- `fre make create-dockerfile [options]`
+   - Purpose: Creates the dockerfile and creates the container (with execute option)
+   - With the creation of the dockerfile, the Makefile, checkout script, and any other necessary script is copied into the container from a temporary location
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+
+- `fre make run-fremake [options]`
+   - Purpose: Create the checkout script, Makefile, compile script, and dockerfile (platform dependent) for the compilation of the model
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+        - `-npc, --no-parallel-checkout (for container build)`
+        - `-j, --jobs [number of jobs to run simultneously]`
+        - `-n, --parallel [number of concurrent modile compiles]`
 
 **Quickstart**
 

From ea331f4b4c7340113841db1416ab04bb3aaa4abe Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:25:06 -0500
Subject: [PATCH 19/39] Update usage.rst

---
 docs/usage.rst | 47 -----------------------------------------------
 1 file changed, 47 deletions(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index 136ae989..e84e566e 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -59,53 +59,6 @@ The fremake canopy fre-cli subcommands are described below ([Subtools](#subtools
 
 Additionally, as mentioned, multiple targets can be used more multiple target-platform combinations.
 
-**Subtools**
-
-- `fre make create-checkout [options]`
-   - Purpose: Creates the checkout script and can check out source code (with execute option)
-   - Options:
-        - `-y, --yamlfile [experiment yaml] (required)`
-        - `-p, --platform [platform] (required)`
-        - `-t, --target [target] (required)`
-        - `-j, --jobs [number of jobs to run simultneously]`
-        - `-npc, --no-parallel-checkout (for container build)`
-        - `-e, --execute`
-
-- `fre make create-makefile [options]`
-   - Purpose: Creates the makefile
-   - Options:
-        - `-y, --yamlfile [experiment yaml] (required)`
-        - `-p, --platform [platform] (required)`
-        - `-t, --target [target] (required)`
-
-- `fre make create-compile [options]`
-   - Purpose: Creates the compile script and compiles the model (with execute option)
-   - Options:
-        - `-y, --yamlfile [experiment yaml] (required)`
-        - `-p, --platform [platform] (required)`
-        - `-t, --target [target] (required)`
-        - `-j, --jobs [number of jobs to run simultneously]`
-        - `-n, --parallel [number of concurrent modile compiles]`
-        - `-e, --execute`
-
-- `fre make create-dockerfile [options]`
-   - Purpose: Creates the dockerfile and creates the container (with execute option)
-   - With the creation of the dockerfile, the Makefile, checkout script, and any other necessary script is copied into the container from a temporary location
-   - Options:
-        - `-y, --yamlfile [experiment yaml] (required)`
-        - `-p, --platform [platform] (required)`
-        - `-t, --target [target] (required)`
-
-- `fre make run-fremake [options]`
-   - Purpose: Create the checkout script, Makefile, compile script, and dockerfile (platform dependent) for the compilation of the model
-   - Options:
-        - `-y, --yamlfile [experiment yaml] (required)`
-        - `-p, --platform [platform] (required)`
-        - `-t, --target [target] (required)`
-        - `-npc, --no-parallel-checkout (for container build)`
-        - `-j, --jobs [number of jobs to run simultneously]`
-        - `-n, --parallel [number of concurrent modile compiles]`
-
 **Quickstart**
 
 1. **Bare-metal Build:**

From 007c21db951b02c4247daf97cfccdbe4e991aed1 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:25:48 -0500
Subject: [PATCH 20/39] Put subtools in here

---
 docs/fre_make.rst | 46 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 43 insertions(+), 3 deletions(-)

diff --git a/docs/fre_make.rst b/docs/fre_make.rst
index 2dab923e..bb6caa2b 100644
--- a/docs/fre_make.rst
+++ b/docs/fre_make.rst
@@ -1,4 +1,44 @@
-.. NEEDS UPDATING #TODO
-1. ``run-fremake``
+1. `fre make create-checkout [options]`
+   - Purpose: Creates the checkout script and can check out source code (with execute option)
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+        - `-j, --jobs [number of jobs to run simultneously]`
+        - `-npc, --no-parallel-checkout (for container build)`
+        - `-e, --execute`
 
-* placehold
+2. `fre make create-makefile [options]`
+   - Purpose: Creates the makefile
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+
+3. `fre make create-compile [options]`
+   - Purpose: Creates the compile script and compiles the model (with execute option)
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+        - `-j, --jobs [number of jobs to run simultneously]`
+        - `-n, --parallel [number of concurrent modile compiles]`
+        - `-e, --execute`
+
+4. `fre make create-dockerfile [options]`
+   - Purpose: Creates the dockerfile and creates the container (with execute option)
+   - With the creation of the dockerfile, the Makefile, checkout script, and any other necessary script is copied into the container from a temporary location
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+
+5. `fre make run-fremake [options]`
+   - Purpose: Create the checkout script, Makefile, compile script, and dockerfile (platform dependent) for the compilation of the model
+   - Options:
+        - `-y, --yamlfile [experiment yaml] (required)`
+        - `-p, --platform [platform] (required)`
+        - `-t, --target [target] (required)`
+        - `-npc, --no-parallel-checkout (for container build)`
+        - `-j, --jobs [number of jobs to run simultneously]`
+        - `-n, --parallel [number of concurrent modile compiles]`

From f91b9663a83dc23dfce4dd9f05c45d33343c7448 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:26:23 -0500
Subject: [PATCH 21/39] Need `include` back in here

---
 docs/usage.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/usage.rst b/docs/usage.rst
index e84e566e..696c33f4 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -45,6 +45,8 @@ Brief rundown of commands also provided below:
 ``fre make``
 ============
 
+.. include:: fre_make.rst
+
 Through the fre-cli, `fre make` can be used to create and run a checkout script, makefile, and compile a model.
 
 * Fremake Canopy Supports:

From 37e0fa4f598d79596d8a3e4fd3182f8b73232317 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:35:16 -0500
Subject: [PATCH 22/39] Update fre_make.rst

---
 docs/fre_make.rst | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/docs/fre_make.rst b/docs/fre_make.rst
index bb6caa2b..bc699661 100644
--- a/docs/fre_make.rst
+++ b/docs/fre_make.rst
@@ -1,4 +1,7 @@
-1. `fre make create-checkout [options]`
+``create-checkout``
+-------------
+
+`fre make create-checkout [options]`
    - Purpose: Creates the checkout script and can check out source code (with execute option)
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
@@ -8,14 +11,20 @@
         - `-npc, --no-parallel-checkout (for container build)`
         - `-e, --execute`
 
-2. `fre make create-makefile [options]`
+``create-makefile`` 
+-------------
+
+`fre make create-makefile [options]`
    - Purpose: Creates the makefile
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
         - `-p, --platform [platform] (required)`
         - `-t, --target [target] (required)`
 
-3. `fre make create-compile [options]`
+``create-compile``
+-------------
+
+`fre make create-compile [options]`
    - Purpose: Creates the compile script and compiles the model (with execute option)
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
@@ -25,7 +34,10 @@
         - `-n, --parallel [number of concurrent modile compiles]`
         - `-e, --execute`
 
-4. `fre make create-dockerfile [options]`
+``create-dockerfile``
+-------------
+
+`fre make create-dockerfile [options]`
    - Purpose: Creates the dockerfile and creates the container (with execute option)
    - With the creation of the dockerfile, the Makefile, checkout script, and any other necessary script is copied into the container from a temporary location
    - Options:
@@ -33,7 +45,10 @@
         - `-p, --platform [platform] (required)`
         - `-t, --target [target] (required)`
 
-5. `fre make run-fremake [options]`
+``run-fremake``
+-------------
+
+`fre make run-fremake [options]`
    - Purpose: Create the checkout script, Makefile, compile script, and dockerfile (platform dependent) for the compilation of the model
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`

From 07e7fb3ba74c196015fc71a0a4d7bdbfff1204ff Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 12:12:41 -0500
Subject: [PATCH 23/39]  Organize guides and quickstarts

---
 docs/quickstarts.rst | 100 ++++++++++++++++++++++++++++++++++++
 docs/tool_guides.rst |  78 ++++++++++++++++++++++++++++
 docs/usage.rst       | 120 +------------------------------------------
 3 files changed, 180 insertions(+), 118 deletions(-)
 create mode 100644 docs/quickstarts.rst
 create mode 100644 docs/tool_guides.rst

diff --git a/docs/quickstarts.rst b/docs/quickstarts.rst
new file mode 100644
index 00000000..640f9d97
--- /dev/null
+++ b/docs/quickstarts.rst
@@ -0,0 +1,100 @@
+``fre app``
+============
+
+``fre catalog``
+============
+
+``fre cmor``
+============
+
+``fre make``
+============
+
+**Quickstart**
+
+1. **Bare-metal Build:**
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create and run the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
+
+2. **Bare-metal Build Multi-target:**
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create and run the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
+
+3. **Container Build:**
+
+In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p hpcme.2023 -t prod
+
+  # Create Dockerfile
+  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod
+
+  # Create and run the Dockerfile
+  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
+
+4. **Run all of fremake:**
+
+.. code-block::
+
+  # Bare-metal
+  fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Container
+  fre make run-fremake -y am5.yaml -p hpcme.2023 -t prod -npc
+
+``fre pp``
+============
+
+``fre yamltools``
+============
+
+``fre check``
+============
+
+``fre list``
+============
+
+``fre run``
+============
+
+``fre test``
+============
diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
new file mode 100644
index 00000000..35957d1b
--- /dev/null
+++ b/docs/tool_guides.rst
@@ -0,0 +1,78 @@
+**Tool Guides**
+
+``fre app``
+============
+
+``fre catalog``
+============
+
+``fre cmor``
+============
+
+.. _reference-name: 
+
+``fre make guide``
+============
+
+1. **Bare-metal Build:**
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y [model yaml file] -p [platform] -t [target]
+
+  # Create and run checkout script
+  fre make create-checkout -y [model yaml file] -p [platform] -t [target] --execute
+
+  # Create Makefile
+  fre make create-makefile -y [model yaml file] -p [platform] -t [target]
+
+  # Creat the compile script
+  fre make create-compile -y [model yaml file] -p [platform] -t [target]
+
+  # Create and run the compile script
+  fre make create-compile -y [model yaml file] -p [platform] -t [target] --execute
+
+  # Run all of fremake
+  fre make run-fremake -y [model yaml file] -p [platform] -t [target] [other options...]
+
+2. **Container Build:**
+
+For the container build, parallel checkouts are not supported, so the `-npc` options must be used for the checkout script. In addition the platform must be a container platform.
+
+***To reiterate, users will not be able to create containers unless they have podman access on gaea.***
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] -npc
+
+  # Create and run checkout script
+  fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
+
+  # Create Makefile
+  fre make create-makefile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target]
+
+  # Create a Dockerfile
+  fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target]
+
+  # Create and run the Dockerfile
+  fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
+
+``fre pp``
+============
+
+``fre yamltools``
+============
+
+``fre check``
+============
+
+``fre list``
+============
+
+``fre run``
+============
+
+``fre test``
+============
diff --git a/docs/usage.rst b/docs/usage.rst
index 696c33f4..d185349e 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -45,8 +45,6 @@ Brief rundown of commands also provided below:
 ``fre make``
 ============
 
-.. include:: fre_make.rst
-
 Through the fre-cli, `fre make` can be used to create and run a checkout script, makefile, and compile a model.
 
 * Fremake Canopy Supports:
@@ -61,123 +59,9 @@ The fremake canopy fre-cli subcommands are described below ([Subtools](#subtools
 
 Additionally, as mentioned, multiple targets can be used more multiple target-platform combinations.
 
-**Quickstart**
-
-1. **Bare-metal Build:**
-
-.. code-block:: 
-
-  # Create checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Create and run checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod --execute
-
-  # Create Makefile
-  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Create the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Create and run the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
-
-2. **Bare-metal Build Multi-target:**
-
-.. code-block:: 
-
-  # Create checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug
-
-  # Create and run checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
-
-  # Create Makefile
-  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
-
-  # Create the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
-
-  # Create and run the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
-
-3. **Container Build:**
-
-In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
-
-.. code-block:: 
-
-  # Create checkout script
-  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc
-
-  # Create and run checkout script
-  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc --execute
-
-  # Create Makefile
-  fre make create-makefile -y am5.yaml -p hpcme.2023 -t prod
-
-  # Create Dockerfile
-  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod
-
-  # Create and run the Dockerfile
-  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
-
-4. **Run all of fremake:**
-
-.. code-block:: 
-
-  # Bare-metal
-  fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Container
-  fre make run-fremake -y am5.yaml -p hpcme.2023 -t prod -npc
-
-**Guide**
-
-1. **Bare-metal Build:**
-
-.. code-block:: 
-
-  # Create checkout script
-  fre make create-checkout -y [model yaml file] -p [platform] -t [target]
-
-  # Create and run checkout script
-  fre make create-checkout -y [model yaml file] -p [platform] -t [target] --execute
-
-  # Create Makefile
-  fre make create-makefile -y [model yaml file] -p [platform] -t [target]
-
-  # Creat the compile script
-  fre make create-compile -y [model yaml file] -p [platform] -t [target]
-
-  # Create and run the compile script
-  fre make create-compile -y [model yaml file] -p [platform] -t [target] --execute
-
-  # Run all of fremake
-  fre make run-fremake -y [model yaml file] -p [platform] -t [target] [other options...]
-
-2. **Container Build:**
-
-For the container build, parallel checkouts are not supported, so the `-npc` options must be used for the checkout script. In addition the platform must be a container platform.
-
-***To reiterate, users will not be able to create containers unless they have podman access on gaea.***
-
-.. code-block:: 
-
-  # Create checkout script
-  fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] -npc
-
-  # Create and run checkout script
-  fre make create-checkout -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
-
-  # Create Makefile
-  fre make create-makefile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target]
-
-  # Create a Dockerfile
-  fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target]
+.. include:: fre_make.rst
 
-  # Create and run the Dockerfile
-  fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
+:ref:`fre-make-guide`
 
 ``fre pp``
 ==========

From e482be0ca715e14603788404a3a41b91feb8a6af Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 12:29:14 -0500
Subject: [PATCH 24/39]  Try to reference correctly

---
 docs/index.rst       | 1 +
 docs/tool_guides.rst | 2 +-
 docs/usage.rst       | 6 +++---
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index 2bf5589e..4f38ffc8 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -14,6 +14,7 @@ Welcome to Fre-Cli's documentation!
 
    setup
    usage
+   guides
    developer_usage
    contributing_to_doc
    badges
diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 35957d1b..46f95077 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -9,7 +9,7 @@
 ``fre cmor``
 ============
 
-.. _reference-name: 
+.. _fre-make-guide: 
 
 ``fre make guide``
 ============
diff --git a/docs/usage.rst b/docs/usage.rst
index d185349e..9ec31007 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -55,13 +55,13 @@ Through the fre-cli, `fre make` can be used to create and run a checkout script,
 
 ** **Note: Users will not be able to create containers without access to podman**
 
-The fremake canopy fre-cli subcommands are described below ([Subtools](#subtools)), as well as a Guide on the order in which to use them ([Guide](#guide)).
-
 Additionally, as mentioned, multiple targets can be used more multiple target-platform combinations.
 
 .. include:: fre_make.rst
 
-:ref:`fre-make-guide`
+Guide:
+
+* :ref:`fre-make-guide`
 
 ``fre pp``
 ==========

From a366de98ced2c0b8363caa0ce1b6d2f9391c13b0 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 12:47:00 -0500
Subject: [PATCH 25/39]  Update references

---
 docs/index.rst       |   2 +-
 docs/quickstarts.rst | 100 -------------------------------------------
 docs/tool_guides.rst |  76 +++++++++++++++++++++++++++++++-
 docs/usage.rst       |   6 ++-
 4 files changed, 79 insertions(+), 105 deletions(-)
 delete mode 100644 docs/quickstarts.rst

diff --git a/docs/index.rst b/docs/index.rst
index 4f38ffc8..f573f1bb 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -14,7 +14,7 @@ Welcome to Fre-Cli's documentation!
 
    setup
    usage
-   guides
+   tool_guides
    developer_usage
    contributing_to_doc
    badges
diff --git a/docs/quickstarts.rst b/docs/quickstarts.rst
deleted file mode 100644
index 640f9d97..00000000
--- a/docs/quickstarts.rst
+++ /dev/null
@@ -1,100 +0,0 @@
-``fre app``
-============
-
-``fre catalog``
-============
-
-``fre cmor``
-============
-
-``fre make``
-============
-
-**Quickstart**
-
-1. **Bare-metal Build:**
-
-.. code-block::
-
-  # Create checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Create and run checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod --execute
-
-  # Create Makefile
-  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Create the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Create and run the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
-
-2. **Bare-metal Build Multi-target:**
-
-.. code-block::
-
-  # Create checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug
-
-  # Create and run checkout script
-  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
-
-  # Create Makefile
-  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
-
-  # Create the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
-
-  # Create and run the compile script
-  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
-
-3. **Container Build:**
-
-In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
-
-.. code-block::
-
-  # Create checkout script
-  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc
-
-  # Create and run checkout script
-  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc --execute
-
-  # Create Makefile
-  fre make create-makefile -y am5.yaml -p hpcme.2023 -t prod
-
-  # Create Dockerfile
-  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod
-
-  # Create and run the Dockerfile
-  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
-
-4. **Run all of fremake:**
-
-.. code-block::
-
-  # Bare-metal
-  fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
-
-  # Container
-  fre make run-fremake -y am5.yaml -p hpcme.2023 -t prod -npc
-
-``fre pp``
-============
-
-``fre yamltools``
-============
-
-``fre check``
-============
-
-``fre list``
-============
-
-``fre run``
-============
-
-``fre test``
-============
diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 46f95077..9aa0bc19 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -9,11 +9,12 @@
 ``fre cmor``
 ============
 
-.. _fre-make-guide: 
 
-``fre make guide``
+``fre make``
 ============
 
+.. _fre-make-guide:
+
 1. **Bare-metal Build:**
 
 .. code-block::
@@ -59,6 +60,77 @@ For the container build, parallel checkouts are not supported, so the `-npc` opt
   # Create and run the Dockerfile
   fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
 
+.. _fre-make-quickstart:
+
+1. **Bare-metal Build:**
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Create and run the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
+
+2. **Bare-metal Build Multi-target:**
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug
+
+  # Create and run the compile script
+  fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
+
+3. **Container Build:**
+
+In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
+
+.. code-block::
+
+  # Create checkout script
+  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc
+
+  # Create and run checkout script
+  fre make create-checkout -y am5.yaml -p hpcme.2023 -t prod -npc --execute
+
+  # Create Makefile
+  fre make create-makefile -y am5.yaml -p hpcme.2023 -t prod
+
+  # Create Dockerfile
+  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod
+
+  # Create and run the Dockerfile
+  fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
+
+4. **Run all of fremake:**
+
+.. code-block::
+
+  # Bare-metal
+  fre make run-fremake -y am5.yaml -p ncrc5.intel23 -t prod
+
+  # Container
+  fre make run-fremake -y am5.yaml -p hpcme.2023 -t prod -npc
+
 ``fre pp``
 ============
 
diff --git a/docs/usage.rst b/docs/usage.rst
index 9ec31007..a02ad21f 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -59,10 +59,12 @@ Additionally, as mentioned, multiple targets can be used more multiple target-pl
 
 .. include:: fre_make.rst
 
-Guide:
-
+Guide to `fre make` subtools:
 * :ref:`fre-make-guide`
 
+Quickstart:
+* :ref:`fre-make-quickstart`
+
 ``fre pp``
 ==========
 

From 40700aa0c7c38dee77c497926581d922d391b5db Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 13:01:29 -0500
Subject: [PATCH 26/39]  Dropdown option?

---
 docs/index.rst       | 5 ++++-
 docs/tool_guides.rst | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index f573f1bb..a7c072cd 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -14,7 +14,10 @@ Welcome to Fre-Cli's documentation!
 
    setup
    usage
-   tool_guides
+
+   .. dropdown:: Tool Guides
+       tool_guides
+
    developer_usage
    contributing_to_doc
    badges
diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 9aa0bc19..6034988d 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -1,4 +1,5 @@
-**Tool Guides**
+Tool Guides
+=============
 
 ``fre app``
 ============

From 0fdfb40a8d1cf7774a56db8110e21eaa65184dd7 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 13:12:23 -0500
Subject: [PATCH 27/39]  Update index.rst

---
 docs/index.rst | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index a7c072cd..f573f1bb 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -14,10 +14,7 @@ Welcome to Fre-Cli's documentation!
 
    setup
    usage
-
-   .. dropdown:: Tool Guides
-       tool_guides
-
+   tool_guides
    developer_usage
    contributing_to_doc
    badges

From 0e1b045bccb7cfd9de5e738f9db41bc84abae69c Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 13:23:35 -0500
Subject: [PATCH 28/39]  Fix link

---
 docs/usage.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/usage.rst b/docs/usage.rst
index a02ad21f..f9ce737a 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -60,9 +60,11 @@ Additionally, as mentioned, multiple targets can be used more multiple target-pl
 .. include:: fre_make.rst
 
 Guide to `fre make` subtools:
+
 * :ref:`fre-make-guide`
 
 Quickstart:
+
 * :ref:`fre-make-quickstart`
 
 ``fre pp``

From 9ba45526cd04a689f35141296fc030de27f9b5c8 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 13:29:20 -0500
Subject: [PATCH 29/39]  Update tool_guides

---
 docs/tool_guides.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 6034988d..4458af29 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -1,6 +1,8 @@
 Tool Guides
 =============
 
+Guides for the process in which subtools are used with tools.
+
 ``fre app``
 ============
 

From a541ea7d6eca2d0813a75495a21ec37b781811d3 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 13:47:12 -0500
Subject: [PATCH 30/39]  Update toold guides

---
 docs/tool_guides.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 4458af29..1280ed80 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -1,8 +1,11 @@
+.. NEEDS UPDATING #TODO
+=============
 Tool Guides
 =============
 
 Guides for the process in which subtools are used with tools.
 
+
 ``fre app``
 ============
 

From bfdabf0042da14a5cf964b7a86bc784495b40bf8 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 14:03:12 -0500
Subject: [PATCH 31/39]  Fix reference link

---
 docs/usage.rst | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index f9ce737a..957459b7 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -60,12 +60,10 @@ Additionally, as mentioned, multiple targets can be used more multiple target-pl
 .. include:: fre_make.rst
 
 Guide to `fre make` subtools:
-
-* :ref:`fre-make-guide`
+:ref:`fre-make-guide`
 
 Quickstart:
-
-* :ref:`fre-make-quickstart`
+:ref:`fre-make-quickstart`
 
 ``fre pp``
 ==========

From f4df6f21ea4578d59754ec79249a944207d7aa1b Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 14:14:53 -0500
Subject: [PATCH 32/39]  Add space

---
 docs/usage.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/usage.rst b/docs/usage.rst
index 957459b7..a99a7c66 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -60,9 +60,11 @@ Additionally, as mentioned, multiple targets can be used more multiple target-pl
 .. include:: fre_make.rst
 
 Guide to `fre make` subtools:
+
 :ref:`fre-make-guide`
 
 Quickstart:
+
 :ref:`fre-make-quickstart`
 
 ``fre pp``

From 0737de7238bd1988e170a2a9fd57b565a9e969ad Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 14:21:36 -0500
Subject: [PATCH 33/39]  Fix links

---
 docs/tool_guides.rst | 4 +---
 docs/usage.rst       | 5 +----
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 1280ed80..ff4b1786 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -15,12 +15,11 @@ Guides for the process in which subtools are used with tools.
 ``fre cmor``
 ============
 
+.. _fre-make-guide:
 
 ``fre make``
 ============
 
-.. _fre-make-guide:
-
 1. **Bare-metal Build:**
 
 .. code-block::
@@ -66,7 +65,6 @@ For the container build, parallel checkouts are not supported, so the `-npc` opt
   # Create and run the Dockerfile
   fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
 
-.. _fre-make-quickstart:
 
 1. **Bare-metal Build:**
 
diff --git a/docs/usage.rst b/docs/usage.rst
index a99a7c66..6a3538f7 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -59,13 +59,10 @@ Additionally, as mentioned, multiple targets can be used more multiple target-pl
 
 .. include:: fre_make.rst
 
-Guide to `fre make` subtools:
+Guide and quickstart to `fre make` subtools:
 
 :ref:`fre-make-guide`
 
-Quickstart:
-
-:ref:`fre-make-quickstart`
 
 ``fre pp``
 ==========

From 9a93a3db925bd2089709c8e2ffdfcf39661fc2b4 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 14:28:27 -0500
Subject: [PATCH 34/39]  Update guide name

---
 docs/tool_guides.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index ff4b1786..3d2ad01f 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -17,7 +17,7 @@ Guides for the process in which subtools are used with tools.
 
 .. _fre-make-guide:
 
-``fre make``
+``fre make guide``
 ============
 
 1. **Bare-metal Build:**

From dd0bf01e8dff4df8f4308f5b1ebec669a011462e Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Fri, 8 Nov 2024 14:35:42 -0500
Subject: [PATCH 35/39]  Update guide format

---
 docs/tool_guides.rst | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 3d2ad01f..19ee0db7 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -20,7 +20,7 @@ Guides for the process in which subtools are used with tools.
 ``fre make guide``
 ============
 
-1. **Bare-metal Build:**
+1. Bare-metal Build:
 
 .. code-block::
 
@@ -42,11 +42,11 @@ Guides for the process in which subtools are used with tools.
   # Run all of fremake
   fre make run-fremake -y [model yaml file] -p [platform] -t [target] [other options...]
 
-2. **Container Build:**
+2. Container Build:
 
 For the container build, parallel checkouts are not supported, so the `-npc` options must be used for the checkout script. In addition the platform must be a container platform.
 
-***To reiterate, users will not be able to create containers unless they have podman access on gaea.***
+Users will not be able to create containers unless they have podman access on gaea.
 
 .. code-block::
 
@@ -66,7 +66,9 @@ For the container build, parallel checkouts are not supported, so the `-npc` opt
   fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
 
 
-1. **Bare-metal Build:**
+** Quickstart **
+
+1. Bare-metal Build:
 
 .. code-block::
 
@@ -85,7 +87,7 @@ For the container build, parallel checkouts are not supported, so the `-npc` opt
   # Create and run the compile script
   fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod --execute
 
-2. **Bare-metal Build Multi-target:**
+2. Bare-metal Build Multi-target:
 
 .. code-block::
 
@@ -104,7 +106,7 @@ For the container build, parallel checkouts are not supported, so the `-npc` opt
   # Create and run the compile script
   fre make create-compile -y am5.yaml -p ncrc5.intel23 -t prod -t debug --execute
 
-3. **Container Build:**
+3. Container Build:
 
 In order for the container to build successfully, a `-npc`, or `--no-parallel-checkout` is needed.
 
@@ -125,7 +127,7 @@ In order for the container to build successfully, a `-npc`, or `--no-parallel-ch
   # Create and run the Dockerfile
   fre make create-dockerfile -y am5.yaml -p hpcme.2023 -t prod --execute
 
-4. **Run all of fremake:**
+4. Run all of fremake:
 
 .. code-block::
 

From 11160fc5dfa0ee55e49e5232fd65478c144ada1a Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Tue, 12 Nov 2024 10:51:26 -0500
Subject: [PATCH 36/39] Update tool_guides.rst

---
 docs/tool_guides.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tool_guides.rst b/docs/tool_guides.rst
index 19ee0db7..9a6459db 100644
--- a/docs/tool_guides.rst
+++ b/docs/tool_guides.rst
@@ -66,7 +66,7 @@ Users will not be able to create containers unless they have podman access on ga
   fre make create-dockerfile -y [model yaml file] -p [CONTAINER PLATFORM] -t [target] --execute
 
 
-** Quickstart **
+**Quickstart**
 
 1. Bare-metal Build:
 

From 17df5cd57a5fc026454a14aa97765e968cf463e3 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@ldt-4742397.gfdl.noaa.gov>
Date: Tue, 12 Nov 2024 12:08:09 -0500
Subject: [PATCH 37/39]  Update format

---
 docs/fre_make.rst | 10 +++++-----
 docs/usage.rst    |  4 +---
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/docs/fre_make.rst b/docs/fre_make.rst
index bc699661..5a3e557b 100644
--- a/docs/fre_make.rst
+++ b/docs/fre_make.rst
@@ -1,7 +1,7 @@
 ``create-checkout``
 -------------
 
-`fre make create-checkout [options]`
+``fre make create-checkout [options]``
    - Purpose: Creates the checkout script and can check out source code (with execute option)
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
@@ -14,7 +14,7 @@
 ``create-makefile`` 
 -------------
 
-`fre make create-makefile [options]`
+``fre make create-makefile [options]``
    - Purpose: Creates the makefile
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
@@ -24,7 +24,7 @@
 ``create-compile``
 -------------
 
-`fre make create-compile [options]`
+``fre make create-compile [options]``
    - Purpose: Creates the compile script and compiles the model (with execute option)
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
@@ -37,7 +37,7 @@
 ``create-dockerfile``
 -------------
 
-`fre make create-dockerfile [options]`
+``fre make create-dockerfile [options]``
    - Purpose: Creates the dockerfile and creates the container (with execute option)
    - With the creation of the dockerfile, the Makefile, checkout script, and any other necessary script is copied into the container from a temporary location
    - Options:
@@ -48,7 +48,7 @@
 ``run-fremake``
 -------------
 
-`fre make run-fremake [options]`
+``fre make run-fremake [options]``
    - Purpose: Create the checkout script, Makefile, compile script, and dockerfile (platform dependent) for the compilation of the model
    - Options:
         - `-y, --yamlfile [experiment yaml] (required)`
diff --git a/docs/usage.rst b/docs/usage.rst
index 69e5dd84..6993e99c 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -55,7 +55,7 @@ intercomparisons (MIPs) using the ``cmor`` module is, quite cleverly, referred t
 
 Through the fre-cli, `fre make` can be used to create and run a checkout script, makefile, and compile a model.
 
-* Fremake Canopy Supports:
+Fremake Canopy Supports:
    - multiple targets; use `-t` flag to define each target
    - bare-metal build
    - container creation
@@ -63,8 +63,6 @@ Through the fre-cli, `fre make` can be used to create and run a checkout script,
 
 ** **Note: Users will not be able to create containers without access to podman**
 
-Additionally, as mentioned, multiple targets can be used more multiple target-platform combinations.
-
 .. include:: fre_make.rst
 
 Guide and quickstart to `fre make` subtools:

From 88f51d1a99b2081af6a01e8e4d97d78ac63c8488 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Tue, 12 Nov 2024 12:58:41 -0500
Subject: [PATCH 38/39] Update publish_conda.yml

---
 .github/workflows/publish_conda.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish_conda.yml b/.github/workflows/publish_conda.yml
index 5815c07d..7a66d746 100644
--- a/.github/workflows/publish_conda.yml
+++ b/.github/workflows/publish_conda.yml
@@ -13,7 +13,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: 'recursive'
- 
       - name: Add mkmf to PATH
         run: |
           echo $PWD/mkmf/bin >> $GITHUB_PATH
@@ -24,4 +23,5 @@ jobs:
           conda install conda-build anaconda-client conda-verify
           export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
           conda config --set anaconda_upload yes
-          conda build .
\ No newline at end of file
+          conda build .
+          

From c826eb72f5158a1d7a8c375378487303995e3c24 Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Tue, 12 Nov 2024 12:59:21 -0500
Subject: [PATCH 39/39] Didn't mean to add space

---
 .github/workflows/publish_conda.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/publish_conda.yml b/.github/workflows/publish_conda.yml
index 7a66d746..26b1825a 100644
--- a/.github/workflows/publish_conda.yml
+++ b/.github/workflows/publish_conda.yml
@@ -24,4 +24,3 @@ jobs:
           export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
           conda config --set anaconda_upload yes
           conda build .
-