From 63375025e03a236ba29abe38a7f29f0677f3e231 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Mon, 9 Feb 2026 11:12:26 +1100
Subject: [PATCH 01/13] Update setup.sh

---
 setup.sh | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/setup.sh b/setup.sh
index 1a49a57..07e9327 100755
--- a/setup.sh
+++ b/setup.sh
@@ -2,12 +2,17 @@
 set -euo pipefail
 
 # Gadi setup for esmf-trace
-module load python3/3.11.7
 module use /g/data/vk83/modules
 module load model-tools/babeltrace2/2.1.2
 
 # Create venv and install
 python3 -m venv .venv
 . .venv/bin/activate
+
+pip install --upgrade pip setuptools wheel
+
 pip install -r requirements.txt
+
+pip install -r requirements-access.txt
+
 pip install -e .

From 6c54e8621f7b4e60436cee5fcce2269a7c2c36bd Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Mon, 9 Feb 2026 11:13:21 +1100
Subject: [PATCH 02/13] Add requirements-access.txt

---
 requirements-access.txt | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 requirements-access.txt

diff --git a/requirements-access.txt b/requirements-access.txt
new file mode 100644
index 0000000..b037881
--- /dev/null
+++ b/requirements-access.txt
@@ -0,0 +1,2 @@
+git+https://github.com/ACCESS-NRI/access-profiling.git@47-om3-profiling_temporary
+git+https://github.com/ACCESS-NRI/access-config-utils.git@32-accessom3-layout

From 32b3f307dc38bac41062382f97abde15e2bf5fad Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Mon, 9 Feb 2026 11:16:37 +1100
Subject: [PATCH 03/13] Update pyproject.toml

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 29f0ad8..20449c4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,9 @@ dependencies = [
   "plotly",
   "matplotlib",
   "ruamel.yaml",
-  "pyarrow"
+  "pyarrow",
+  "experiment-generator",
+  "experiment-runner"
 ]
 
 [build-system]

From aab2873f775a775c33e63e43828123479085fbc1 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Wed, 11 Feb 2026 14:17:52 +1100
Subject: [PATCH 04/13] keep experiment-generator and experiment-runner as an
 extra bundle

---
 pyproject.toml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 20449c4..561ae0b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,8 +21,6 @@ dependencies = [
   "matplotlib",
   "ruamel.yaml",
   "pyarrow",
-  "experiment-generator",
-  "experiment-runner"
 ]
 
 [build-system]
@@ -57,6 +55,11 @@ addopts = [
 ]
 testpaths = ["tests"]
 
+access = [
+  "experiment-generator",
+  "experiment-runner",
+]
+
 [tool.coverage.run]
 
 [tool.ruff]

From 17bde313143009c20aad4c40958bd8364950a9d9 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Wed, 11 Feb 2026 14:24:39 +1100
Subject: [PATCH 05/13] Update associated setup.sh

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

diff --git a/setup.sh b/setup.sh
index 07e9327..edcbc61 100755
--- a/setup.sh
+++ b/setup.sh
@@ -13,6 +13,10 @@ pip install --upgrade pip setuptools wheel
 
 pip install -r requirements.txt
 
+# These are not merged yet, but we want to be able to install them in the meantime,
+# because they are needed for the ARE work.
 pip install -r requirements-access.txt
 
+# Install and try to pull the "access" extras if available
 pip install -e .
+pip install -e ".[access]" || true

From 409f9a97c80c1d1561fc3983368485cd2e1c5623 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Wed, 11 Feb 2026 14:43:14 +1100
Subject: [PATCH 06/13] ruff is not needed in devel

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 561ae0b..f25dfa9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,7 +38,6 @@ Homepage = "https://github.com/ACCESS-NRI/esmf-trace"
 
 [project.optional-dependencies]
 devel = [
-    "ruff",
     "pre-commit",
 ]
 test = [

From 896483ef609863853938cdb4606eaa4a90d39e9c Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Thu, 12 Feb 2026 14:43:42 +1100
Subject: [PATCH 07/13] Remove the optional access section & add an interactive
 section

---
 pyproject.toml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f25dfa9..40667a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,6 +16,8 @@ classifiers = [
 ]
 
 dependencies = [
+  "numpy",
+  "xarray",
   "pandas",
   "plotly",
   "matplotlib",
@@ -40,11 +42,18 @@ Homepage = "https://github.com/ACCESS-NRI/esmf-trace"
 devel = [
     "pre-commit",
 ]
+
 test = [
     "pytest",
     "pytest-cov",
 ]
 
+# Not required for the package but useful for users running notebooks
+interactive = [
+    "jupyter",
+    "ipykernel",
+]
+
 [tool.pytest.ini_options]
 addopts = [
   "--cov=esmf_trace",
@@ -52,12 +61,8 @@ addopts = [
   "--cov-report=html",
   "--cov-report=xml"
 ]
-testpaths = ["tests"]
 
-access = [
-  "experiment-generator",
-  "experiment-runner",
-]
+testpaths = ["tests"]
 
 [tool.coverage.run]
 

From 77848d1a4140d5a8b809ad14860cdbdbf5000e65 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Thu, 12 Feb 2026 14:47:44 +1100
Subject: [PATCH 08/13] Remove requirements.txt

---
 requirements.txt | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index a8e78ee..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pandas
-pyarrow
-numpy
-xarray
-matplotlib
-jupyter

From 8ccea0588a5d10e50dd33bd4072ddd295b038b2b Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Thu, 12 Feb 2026 14:54:00 +1100
Subject: [PATCH 09/13] Update requirements-access.txt

---
 requirements-access.txt | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/requirements-access.txt b/requirements-access.txt
index b037881..7a952eb 100644
--- a/requirements-access.txt
+++ b/requirements-access.txt
@@ -1,2 +1,17 @@
+# Workspace environment for ACCESS profiling and scaling workflows.
+#
+# This file installs multiple ACCESS repos into a single virtual
+# environment for convenient imports and interactive development.
+#
+# It is not intended to represent the runtime requirements of any single
+# repo. Instead, it defines a curated workspace environment that
+# allows multiple tools to be used together.
+
+git+https://github.com/ACCESS-NRI/access-experiment-generator.git@main
+git+https://github.com/ACCESS-NRI/access-experiment-runner.git@main
+
+# These two repos are required for profiling workflows, but are not
+# yet merged into their respective main branches. We therefore install from
+# the relevant feature branches.
 git+https://github.com/ACCESS-NRI/access-profiling.git@47-om3-profiling_temporary
 git+https://github.com/ACCESS-NRI/access-config-utils.git@32-accessom3-layout

From fd47a75893ec9c6897c3d224db7cabab11334a16 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Thu, 12 Feb 2026 14:58:33 +1100
Subject: [PATCH 10/13] Update setup.sh

---
 setup.sh | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/setup.sh b/setup.sh
index edcbc61..93392e3 100755
--- a/setup.sh
+++ b/setup.sh
@@ -11,12 +11,11 @@ python3 -m venv .venv
 
 pip install --upgrade pip setuptools wheel
 
-pip install -r requirements.txt
+# Install the package in editable mode for development
+pip install -e .
 
-# These are not merged yet, but we want to be able to install them in the meantime,
-# because they are needed for the ARE work.
-pip install -r requirements-access.txt
+# Install the interactive tooling for the notebooks
+pip install -e ".[interactive]"
 
-# Install and try to pull the "access" extras if available
-pip install -e .
-pip install -e ".[access]" || true
+# Workspace bundle: install other ACCESS repos into the same venv for workflow convenience
+pip install -r requirements-access.txt

From b026f40f697e1a57d130c12baa2346e5cc6b8130 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Thu, 12 Feb 2026 15:06:25 +1100
Subject: [PATCH 11/13] Update requirements-access.txt

---
 requirements-access.txt | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/requirements-access.txt b/requirements-access.txt
index 7a952eb..82c1c2b 100644
--- a/requirements-access.txt
+++ b/requirements-access.txt
@@ -10,8 +10,6 @@
 git+https://github.com/ACCESS-NRI/access-experiment-generator.git@main
 git+https://github.com/ACCESS-NRI/access-experiment-runner.git@main
 
-# These two repos are required for profiling workflows, but are not
-# yet merged into their respective main branches. We therefore install from
-# the relevant feature branches.
-git+https://github.com/ACCESS-NRI/access-profiling.git@47-om3-profiling_temporary
-git+https://github.com/ACCESS-NRI/access-config-utils.git@32-accessom3-layout
+# Feature branches required for profiling work (not yet merged)
+-e git+https://github.com/ACCESS-NRI/access-profiling.git@47-om3-profiling_temporary#egg=access-profiling
+-e git+https://github.com/ACCESS-NRI/access-config-utils.git@32-accessom3-layout#egg=access-config-utils

From 7bef3fee30c30bce93a1ae24071c728dbdb9d123 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:33:26 +1100
Subject: [PATCH 12/13] rename setup.sh to setup_gadi.sh

---
 setup.sh => setup_gadi.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename setup.sh => setup_gadi.sh (100%)

diff --git a/setup.sh b/setup_gadi.sh
similarity index 100%
rename from setup.sh
rename to setup_gadi.sh

From adc4a985c52b1697675b6db4f533fb4a22f2faf1 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Fri, 13 Feb 2026 13:48:44 +1100
Subject: [PATCH 13/13] add devel to install esmf-trace

---
 setup_gadi.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup_gadi.sh b/setup_gadi.sh
index 93392e3..f40d96d 100755
--- a/setup_gadi.sh
+++ b/setup_gadi.sh
@@ -12,7 +12,7 @@ python3 -m venv .venv
 pip install --upgrade pip setuptools wheel
 
 # Install the package in editable mode for development
-pip install -e .
+pip install -e ".[devel]"
 
 # Install the interactive tooling for the notebooks
 pip install -e ".[interactive]"