From d83f3fb4cc4785535f5ec711c9c99dec46357608 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Wed, 14 Feb 2024 10:43:46 -0500
Subject: [PATCH 01/26] Add initial changes for issue 59 refactor of build
 system

* Remove hardcoded version (which will be replaced dynamically)
* Add specific lines to init
* Add scripts directory, which contains a few helpers
---
 gpax/__init__.py          |  7 +++++++
 gpax/__version__.py       |  1 -
 scripts/LICENSE           | 29 +++++++++++++++++++++++++++++
 scripts/README.md         |  7 +++++++
 scripts/build_docs.sh     | 25 +++++++++++++++++++++++++
 scripts/build_project.sh  |  6 ++++++
 scripts/install.sh        | 27 +++++++++++++++++++++++++++
 scripts/update_version.sh | 35 +++++++++++++++++++++++++++++++++++
 8 files changed, 136 insertions(+), 1 deletion(-)
 delete mode 100644 gpax/__version__.py
 create mode 100644 scripts/LICENSE
 create mode 100644 scripts/README.md
 create mode 100644 scripts/build_docs.sh
 create mode 100644 scripts/build_project.sh
 create mode 100644 scripts/install.sh
 create mode 100644 scripts/update_version.sh

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 7529e8f..f40247c 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -10,3 +10,10 @@
 __all__ = ["utils", "kernels", "mtkernels", "acquisition", "ExactGP", "vExactGP", "DKL",
            "viDKL", "iBNN", "vi_iBNN", "MultiTaskGP", "viMTDKL", "viGP", "sPM", "VarNoiseGP",
            "UIGP", "MeasuredNoiseGP", "viSparseGP", "CoregGP", "sample_next", "__version__"]
+
+# DO NOT CHANGE BELOW ---------------------------------------------------------
+# This is replaced at build time automatically during deployment and
+# installation. Replacing anything will mess that up and crash the entire
+# build.
+__version__ = ...  # semantic-version-placeholder
+# DO NOT CHANGE ABOVE ---------------------------------------------------------
diff --git a/gpax/__version__.py b/gpax/__version__.py
deleted file mode 100644
index 0f29d8c..0000000
--- a/gpax/__version__.py
+++ /dev/null
@@ -1 +0,0 @@
-version = '0.1.7'
diff --git a/scripts/LICENSE b/scripts/LICENSE
new file mode 100644
index 0000000..deacfc5
--- /dev/null
+++ b/scripts/LICENSE
@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2022, Brookhaven Science Associates, LLC, Brookhaven National Laboratory
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/scripts/README.md b/scripts/README.md
new file mode 100644
index 0000000..6f2bd92
--- /dev/null
+++ b/scripts/README.md
@@ -0,0 +1,7 @@
+# Scripts
+
+This directory contains helper scripts for GPax.
+
+- Build scripts for building the project
+- Testing script for the notebook smoke tests
+- `LICENSE` file, attributing code in this directory only to Brookhaven Science Associates (location from which the code was sourced)
diff --git a/scripts/build_docs.sh b/scripts/build_docs.sh
new file mode 100644
index 0000000..d42d820
--- /dev/null
+++ b/scripts/build_docs.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+build_docs () {
+
+    if [[ "${GITHUB_ACTION_IS_RUNNING}" = 1 ]]; then
+        bash scripts/install.sh doc
+    fi
+
+    make -C docs/ html
+
+    # Helper when running on local. If not running in a GitHub Actions
+    # environment, this will attempt to open index.html with the users'
+    # default program
+    if [[ -z "${GITHUB_ACTION_IS_RUNNING}" ]]; then
+        open docs/build/html/index.html
+    fi
+    
+}
+
+pip install toml
+bash scripts/install.sh
+bash scripts/install.sh doc
+bash scripts/update_version.sh set
+build_docs
+bash scripts/update_version.sh reset
diff --git a/scripts/build_project.sh b/scripts/build_project.sh
new file mode 100644
index 0000000..0d5f6f8
--- /dev/null
+++ b/scripts/build_project.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+pip install flit~=3.7
+bash scripts/update_version.sh set
+flit build
+bash scripts/update_version.sh reset
diff --git a/scripts/install.sh b/scripts/install.sh
new file mode 100644
index 0000000..f4cf1f5
--- /dev/null
+++ b/scripts/install.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# Good stuff. The poor man's toml parser
+# https://github.com/pypa/pip/issues/8049
+# This is the analog of pip install -e ".[...]" since for whatever reason
+# it does not appear to work cleanly with pip
+install_doc_requirements_only () {
+    python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["optional-dependencies"]["doc"]))' | pip install -r /dev/stdin
+}
+
+install_test_requirements_only () {
+    python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["optional-dependencies"]["test"]))' | pip install -r /dev/stdin
+}
+
+install_requirements() {
+    python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin
+}
+
+
+pip install toml
+if [ "$1" = "doc" ]; then
+    install_doc_requirements_only
+elif [ "$1" = "test" ]; then
+    install_test_requirements_only
+else
+    install_requirements
+fi
diff --git a/scripts/update_version.sh b/scripts/update_version.sh
new file mode 100644
index 0000000..0bd018e
--- /dev/null
+++ b/scripts/update_version.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+PACKAGE_NAME="gpax"
+
+replace_version_in_init () {
+    pip install dunamai~=1.12
+    version="$(dunamai from git --style pep440 --no-metadata)"
+    dunamai check "$version" --style pep440
+    sed_command="s/...  # semantic-version-placeholder/'$version'/g"
+    if [[ "$OSTYPE" == "darwin"* ]]; then
+        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
+    else
+        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
+    fi
+    echo "__init__ version set to" "$version"
+    export _TMP_VERSION="$version"
+}
+
+reset_version_to_ellipsis () {
+    current_version=$(grep "__version__" "$PACKAGE_NAME"/__init__.py)
+    sed_command="s/$current_version/__version__ = ...  # semantic-version-placeholder/g"
+    if [[ "$OSTYPE" == "darwin"* ]]; then
+        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
+    else
+        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
+    fi
+    echo "$current_version" "reset to placeholder"
+}
+
+
+if [ "$1" == "set" ]; then
+    replace_version_in_init
+elif [ "$1" == "reset" ]; then
+    reset_version_to_ellipsis
+fi

From ff920c41cc383a7df8dc0aa7edef7943040ddb0b Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Wed, 14 Feb 2024 16:41:57 -0500
Subject: [PATCH 02/26] Update pyproject, ignore some IDE tools

---
 .gitignore         |  3 +++
 pyproject.toml     | 41 +++++++++++++++++++++++++++++++++++++++++
 scripts/install.sh |  7 +------
 3 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/.gitignore b/.gitignore
index b6e4761..c0fb41c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Pyright
+pyrightconfig.json
diff --git a/pyproject.toml b/pyproject.toml
index 1eeed4c..6091e9b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,44 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "gpax"
+authors = [
+    {"name" = "Maxim Ziatdinov", "email" = "maxim.ziatdinov@ai4microcopy.com"}
+]
+readme = "README.md"
+requires-python = ">=3.9"
+license = {"file" = "LICENSE"}
+description='Gaussian processes in NumPyro and JAX'
+classifiers=[
+    'Programming Language :: Python',
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Science/Research',
+    'Operating System :: POSIX :: Linux',
+    'Operating System :: MacOS :: MacOS X',
+    'Topic :: Scientific/Engineering'
+]
+
+# Core dependencies
+dependencies = [
+    "matplotlib>=3.1.1",
+    "jax>=0.4.8",
+    "numpyro>=0.11.0",
+    "dm-haiku>=0.0.5",
+    "jaxopt", # TODO: do we want to require this?
+]
+
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = [
+    "flake8",
+    "jaxlib",
+    "pytest",
+    "pytest-cov",
+]
+
 [tool.black]
 line-length = 127
 include = '\.pyi?$'
diff --git a/scripts/install.sh b/scripts/install.sh
index f4cf1f5..bbd3224 100644
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -4,9 +4,6 @@
 # https://github.com/pypa/pip/issues/8049
 # This is the analog of pip install -e ".[...]" since for whatever reason
 # it does not appear to work cleanly with pip
-install_doc_requirements_only () {
-    python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["optional-dependencies"]["doc"]))' | pip install -r /dev/stdin
-}
 
 install_test_requirements_only () {
     python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["optional-dependencies"]["test"]))' | pip install -r /dev/stdin
@@ -18,9 +15,7 @@ install_requirements() {
 
 
 pip install toml
-if [ "$1" = "doc" ]; then
-    install_doc_requirements_only
-elif [ "$1" = "test" ]; then
+if [ "$1" = "test" ]; then
     install_test_requirements_only
 else
     install_requirements

From 0e610b110587bfd5e0fc4483492ac064af95294d Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 08:15:26 -0500
Subject: [PATCH 03/26] Remove old version code in init, remove setup.py

---
 gpax/__init__.py |  1 -
 setup.py         | 40 ----------------------------------------
 2 files changed, 41 deletions(-)
 delete mode 100644 setup.py

diff --git a/gpax/__init__.py b/gpax/__init__.py
index f40247c..10ceef4 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -1,4 +1,3 @@
-from .__version__ import version as __version__
 from . import utils
 from . import kernels
 from . import acquisition
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 537b639..0000000
--- a/setup.py
+++ /dev/null
@@ -1,40 +0,0 @@
-__author__ = "Maxim Ziatdinov"
-__copyright__ = "Copyright Maxim Ziatdinov (2021)"
-__maintainer__ = "Maxim Ziatdinov"
-__email__ = "maxim.ziatdinov@ai4microcopy.com"
-
-from setuptools import setup, find_packages
-import os
-
-module_dir = os.path.dirname(os.path.abspath(__file__))
-
-with open(os.path.join(module_dir, 'gpax/__version__.py')) as f:
-    __version__ = f.read().split("'")[1]
-
-if __name__ == "__main__":
-    setup(
-        name='gpax',
-        python_requires='>=3.9',
-        version=__version__,
-        description='Gaussian processes in NumPyro and JAX',
-        long_description=open(os.path.join(module_dir, 'README.md')).read(),
-        long_description_content_type='text/markdown',
-        url='https://github.com/ziatdinovmax/gpax/',
-        author='Maxim Ziatdinov',
-        author_email='maxim.ziatdinov@ai4microcopy.com',
-        license='MIT license',
-        packages=find_packages(),
-        zip_safe=False,
-        install_requires=[
-            'jax>=0.4.8',
-            'numpyro>=0.11.0',
-            'dm-haiku>=0.0.5',
-            'matplotlib>=3.1'
-        ],
-        classifiers=['Programming Language :: Python',
-                     'Development Status :: 3 - Alpha',
-                     'Intended Audience :: Science/Research',
-                     'Operating System :: POSIX :: Linux',
-                     'Operating System :: MacOS :: MacOS X',
-                     'Topic :: Scientific/Engineering']
-    )

From e6b1a51663516e82c73525c099a3df67e1e8a753 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 08:19:08 -0500
Subject: [PATCH 04/26] Reformat __init__

---
 gpax/__init__.py | 36 +++++++++++++++++++++++++++---------
 1 file changed, 27 insertions(+), 9 deletions(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 10ceef4..36b28cd 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -1,14 +1,32 @@
-from . import utils
-from . import kernels
-from . import acquisition
+from . import acquisition, kernels, utils
 from .hypo import sample_next
-from .models import (DKL, CoregGP, ExactGP, MultiTaskGP, iBNN, vExactGP,
-                     vi_iBNN, viDKL, viGP, sPM, viMTDKL, VarNoiseGP, UIGP,
-                     MeasuredNoiseGP, viSparseGP)
+from .models import (DKL, UIGP, CoregGP, ExactGP, MeasuredNoiseGP, MultiTaskGP,
+                     VarNoiseGP, iBNN, sPM, vExactGP, vi_iBNN, viDKL, viGP,
+                     viMTDKL, viSparseGP)
 
-__all__ = ["utils", "kernels", "mtkernels", "acquisition", "ExactGP", "vExactGP", "DKL",
-           "viDKL", "iBNN", "vi_iBNN", "MultiTaskGP", "viMTDKL", "viGP", "sPM", "VarNoiseGP",
-           "UIGP", "MeasuredNoiseGP", "viSparseGP", "CoregGP", "sample_next", "__version__"]
+__all__ = [
+    "utils",
+    "kernels",
+    "mtkernels",
+    "acquisition",
+    "ExactGP",
+    "vExactGP",
+    "DKL",
+    "viDKL",
+    "iBNN",
+    "vi_iBNN",
+    "MultiTaskGP",
+    "viMTDKL",
+    "viGP",
+    "sPM",
+    "VarNoiseGP",
+    "UIGP",
+    "MeasuredNoiseGP",
+    "viSparseGP",
+    "CoregGP",
+    "sample_next",
+    "__version__",
+]
 
 # DO NOT CHANGE BELOW ---------------------------------------------------------
 # This is replaced at build time automatically during deployment and

From 73bedcea7c2369774dc03010949289e1f0a50623 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 14:09:49 -0500
Subject: [PATCH 05/26] Add dunamai support for if version is not set by build
 system

---
 gpax/__init__.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 36b28cd..dd1e792 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -34,3 +34,15 @@
 # build.
 __version__ = ...  # semantic-version-placeholder
 # DO NOT CHANGE ABOVE ---------------------------------------------------------
+
+# Useful for local development
+if __version__ == ...:
+    try:
+        from dunamai import Version
+        version = Version.from_any_vcs()
+        __version__ = version.serialize()
+    except ImportError:
+        print("You are running a local copy of gpax (not installed via pip)")
+        print("__version__ = ...; pip install dunamai to track local version")
+        pass
+    

From 8bda8562009e06d3c6dbeba096c6aa0c8626dccd Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 14:12:29 -0500
Subject: [PATCH 06/26] Update github actions files

---
 .github/workflows/actions.yml | 11 ++-----
 .github/workflows/ci.yml      | 12 ++++++++
 .github/workflows/unit.yml    | 54 +++++++++++++++++++++++++++++++++++
 3 files changed, 68 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/ci.yml
 create mode 100644 .github/workflows/unit.yml

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 3183a4f..62021c1 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -1,17 +1,10 @@
-name: build
+name: build/test
 
 env:
   PYTHON_MAIN_VERSION: 3.9
   
 on:
-  pull_request:
-    branches:
-      - '*'
-  push:
-    branches:
-      - '*'
-    tags:
-        - '*'
+  workflow_call:
 
 jobs:
   build-linux:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..39e8c90
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,12 @@
+name: CI
+
+on:
+
+  pull_request:
+    branches: ["master", "dev/*", issue-59]
+
+  push:
+    branches: ["master", "dev/*", issue-59]
+
+  unit:
+    uses: ./.github/workflows/unit.yml
diff --git a/.github/workflows/unit.yml b/.github/workflows/unit.yml
new file mode 100644
index 0000000..d7b69d0
--- /dev/null
+++ b/.github/workflows/unit.yml
@@ -0,0 +1,54 @@
+name: Unit
+
+env:
+  PYTHON_MAIN_VERSION: 3.9
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          bash scripts/install.sh
+          bash scripts/install.sh test
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Run tests
+        run: |
+          pytest -v --cov --cov-report xml tests
+
+      - name: Upload coverage to Codecov
+        if: ${{ matrix.python-version == env.PYTHON_MAIN_VERSION }}
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          # directory: ./coverage/reports/
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: true
+          # path_to_write_report: ./coverage/codecov_report.txt
+          verbose: true

From 1290690af71dd84939d2baee4898d7c762a688b7 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 14:16:00 -0500
Subject: [PATCH 07/26] Add some more useful comments to __init__

---
 gpax/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index dd1e792..7a7c304 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -29,13 +29,14 @@
 ]
 
 # DO NOT CHANGE BELOW ---------------------------------------------------------
+# ALSO DO NOT CALL __version__ ANYWHERE ABOVE THIS
 # This is replaced at build time automatically during deployment and
 # installation. Replacing anything will mess that up and crash the entire
 # build.
 __version__ = ...  # semantic-version-placeholder
 # DO NOT CHANGE ABOVE ---------------------------------------------------------
 
-# Useful for local development
+# Silly hack. Useful for local development
 if __version__ == ...:
     try:
         from dunamai import Version

From 56523037eaa779c1c3dc7be596691a29e1b9a143 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 14:16:17 -0500
Subject: [PATCH 08/26] Change update version script to only grep first
 instance

---
 scripts/update_version.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/update_version.sh b/scripts/update_version.sh
index 0bd018e..db98116 100644
--- a/scripts/update_version.sh
+++ b/scripts/update_version.sh
@@ -17,7 +17,8 @@ replace_version_in_init () {
 }
 
 reset_version_to_ellipsis () {
-    current_version=$(grep "__version__" "$PACKAGE_NAME"/__init__.py)
+    # we only grep the first instance of __version__
+    current_version=$(grep -m 1 "__version__" "$PACKAGE_NAME"/__init__.py)
     sed_command="s/$current_version/__version__ = ...  # semantic-version-placeholder/g"
     if [[ "$OSTYPE" == "darwin"* ]]; then
         sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py

From adb0676a13802a51ce922af9ab0168c95f050fa5 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 14:27:51 -0500
Subject: [PATCH 09/26] Make the update version script a bit more robust

---
 scripts/update_version.sh | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/scripts/update_version.sh b/scripts/update_version.sh
index db98116..ac0e0e6 100644
--- a/scripts/update_version.sh
+++ b/scripts/update_version.sh
@@ -1,16 +1,21 @@
 #!/bin/bash
 
 PACKAGE_NAME="gpax"
+SEMANTIC_PLACEHOLDER="...  # semantic-version-placeholder/"
+INIT_FILE_NAME="$PACKAGE_NAME"/__init__.py
+
+
 
 replace_version_in_init () {
     pip install dunamai~=1.12
     version="$(dunamai from git --style pep440 --no-metadata)"
     dunamai check "$version" --style pep440
-    sed_command="s/...  # semantic-version-placeholder/'$version'/g"
+    sed_command="s/'$SEMANTIC_PLACEHOLDER'/'$version'/g"
+    cp "$INIT_FILE_NAME" "$INIT_FILE_NAME".bak
     if [[ "$OSTYPE" == "darwin"* ]]; then
-        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
+        sed -i '' "$sed_command" "$INIT_FILE_NAME"
     else
-        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
+        sed -i "$sed_command" "$INIT_FILE_NAME"
     fi
     echo "__init__ version set to" "$version"
     export _TMP_VERSION="$version"
@@ -18,13 +23,9 @@ replace_version_in_init () {
 
 reset_version_to_ellipsis () {
     # we only grep the first instance of __version__
-    current_version=$(grep -m 1 "__version__" "$PACKAGE_NAME"/__init__.py)
-    sed_command="s/$current_version/__version__ = ...  # semantic-version-placeholder/g"
-    if [[ "$OSTYPE" == "darwin"* ]]; then
-        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
-    else
-        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
-    fi
+    current_version=$(grep -m 1 "__version__" "$INIT_FILE_NAME"/__init__.py)
+    cp "$INIT_FILE_NAME".bak "$INIT_FILE_NAME"
+    rm "$INIT_FILE_NAME".bak
     echo "$current_version" "reset to placeholder"
 }
 

From 0ffa91eab4d94a3781de514075ecadb5a61f1acc Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 15:48:23 -0500
Subject: [PATCH 10/26] Debug update_version

---
 scripts/update_version.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/update_version.sh b/scripts/update_version.sh
index ac0e0e6..82d7267 100644
--- a/scripts/update_version.sh
+++ b/scripts/update_version.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 PACKAGE_NAME="gpax"
-SEMANTIC_PLACEHOLDER="...  # semantic-version-placeholder/"
+SEMANTIC_PLACEHOLDER="...  # semantic-version-placeholder"
 INIT_FILE_NAME="$PACKAGE_NAME"/__init__.py
 
 
@@ -11,6 +11,7 @@ replace_version_in_init () {
     version="$(dunamai from git --style pep440 --no-metadata)"
     dunamai check "$version" --style pep440
     sed_command="s/'$SEMANTIC_PLACEHOLDER'/'$version'/g"
+    echo "$sed_command"
     cp "$INIT_FILE_NAME" "$INIT_FILE_NAME".bak
     if [[ "$OSTYPE" == "darwin"* ]]; then
         sed -i '' "$sed_command" "$INIT_FILE_NAME"

From 8ee711617137d5602197a2a184268b1a5fa1e664 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 15:58:20 -0500
Subject: [PATCH 11/26] Debug update_version

---
 gpax/__init__.py          |  1 -
 scripts/update_version.sh | 22 ++++++++++------------
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 7a7c304..f6631f1 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -25,7 +25,6 @@
     "viSparseGP",
     "CoregGP",
     "sample_next",
-    "__version__",
 ]
 
 # DO NOT CHANGE BELOW ---------------------------------------------------------
diff --git a/scripts/update_version.sh b/scripts/update_version.sh
index 82d7267..db98116 100644
--- a/scripts/update_version.sh
+++ b/scripts/update_version.sh
@@ -1,22 +1,16 @@
 #!/bin/bash
 
 PACKAGE_NAME="gpax"
-SEMANTIC_PLACEHOLDER="...  # semantic-version-placeholder"
-INIT_FILE_NAME="$PACKAGE_NAME"/__init__.py
-
-
 
 replace_version_in_init () {
     pip install dunamai~=1.12
     version="$(dunamai from git --style pep440 --no-metadata)"
     dunamai check "$version" --style pep440
-    sed_command="s/'$SEMANTIC_PLACEHOLDER'/'$version'/g"
-    echo "$sed_command"
-    cp "$INIT_FILE_NAME" "$INIT_FILE_NAME".bak
+    sed_command="s/...  # semantic-version-placeholder/'$version'/g"
     if [[ "$OSTYPE" == "darwin"* ]]; then
-        sed -i '' "$sed_command" "$INIT_FILE_NAME"
+        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
     else
-        sed -i "$sed_command" "$INIT_FILE_NAME"
+        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
     fi
     echo "__init__ version set to" "$version"
     export _TMP_VERSION="$version"
@@ -24,9 +18,13 @@ replace_version_in_init () {
 
 reset_version_to_ellipsis () {
     # we only grep the first instance of __version__
-    current_version=$(grep -m 1 "__version__" "$INIT_FILE_NAME"/__init__.py)
-    cp "$INIT_FILE_NAME".bak "$INIT_FILE_NAME"
-    rm "$INIT_FILE_NAME".bak
+    current_version=$(grep -m 1 "__version__" "$PACKAGE_NAME"/__init__.py)
+    sed_command="s/$current_version/__version__ = ...  # semantic-version-placeholder/g"
+    if [[ "$OSTYPE" == "darwin"* ]]; then
+        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
+    else
+        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
+    fi
     echo "$current_version" "reset to placeholder"
 }
 

From cf5bd0deb6af877ebb8287a37943fe1e09f6b4fe Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 15:59:39 -0500
Subject: [PATCH 12/26] Debug update_version

---
 gpax/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index f6631f1..72d5ec7 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -28,7 +28,7 @@
 ]
 
 # DO NOT CHANGE BELOW ---------------------------------------------------------
-# ALSO DO NOT CALL __version__ ANYWHERE ABOVE THIS
+# ALSO DO NOT TYPE dunder version ANYWHERE ABOVE THIS
 # This is replaced at build time automatically during deployment and
 # installation. Replacing anything will mess that up and crash the entire
 # build.

From 1a8624c2d9099a4f256e8af926dad80e0b3b1a98 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 16:12:49 -0500
Subject: [PATCH 13/26] Update and refactor actions

---
 .github/workflows/actions.yml        | 67 ----------------------------
 .github/workflows/ci.yml             |  7 ++-
 .github/workflows/notebook_smoke.yml | 24 +---------
 scripts/test_notebooks.sh            |  4 +-
 4 files changed, 10 insertions(+), 92 deletions(-)
 delete mode 100644 .github/workflows/actions.yml

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
deleted file mode 100644
index 62021c1..0000000
--- a/.github/workflows/actions.yml
+++ /dev/null
@@ -1,67 +0,0 @@
-name: build/test
-
-env:
-  PYTHON_MAIN_VERSION: 3.9
-  
-on:
-  workflow_call:
-
-jobs:
-  build-linux:
-    
-    strategy:
-      max-parallel: 5
-      matrix:
-        python-version: ['3.9', '3.10', '3.11']
-        os: [ubuntu-latest]
-
-    runs-on: ${{ matrix.os }}
-
-    steps:
-    - uses: actions/checkout@v2
-      
-    - name: Set up Python ${{ matrix.python-version }}
-      
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        sudo apt-get update -qq
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python -m pip install jaxlib
-        python -m pip install jax
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-            
-    - name: install package
-      run: |
-        pip install .
-        pip list
-    
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    
-    - name: Generate coverage report
-      run: |
-        pip install pytest
-        pip install pytest-cov
-        pytest --cov=./ --cov-report=xml
-        
-    - name: Upload coverage to Codecov
-      if: ${{ matrix.python-version == env.PYTHON_MAIN_VERSION }}
-      uses: codecov/codecov-action@v1
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        files: ./coverage.xml
-        # directory: ./coverage/reports/
-        flags: unittests
-        env_vars: OS,PYTHON
-        name: codecov-umbrella
-        fail_ci_if_error: true
-        # path_to_write_report: ./coverage/codecov_report.txt
-        verbose: true
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 39e8c90..c8ff29b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,10 +3,13 @@ name: CI
 on:
 
   pull_request:
-    branches: ["master", "dev/*", issue-59]
+    branches: ["master", "dev/*", mc/issue-59]
 
   push:
-    branches: ["master", "dev/*", issue-59]
+    branches: ["master", "dev/*", mc/issue-59]
 
   unit:
     uses: ./.github/workflows/unit.yml
+
+  notebooks:
+    uses: ./.github/workflows/notebook_smoke.yml
diff --git a/.github/workflows/notebook_smoke.yml b/.github/workflows/notebook_smoke.yml
index 312a5df..a6d8ab7 100644
--- a/.github/workflows/notebook_smoke.yml
+++ b/.github/workflows/notebook_smoke.yml
@@ -4,14 +4,7 @@ env:
   CI_SMOKE: True
 
 on:
-  pull_request:
-    branches:
-      - '*'
-  push:
-    branches:
-      - '*'
-    tags:
-      - '*'
+  workflow_call:
 
 jobs:
   build-linux:
@@ -34,22 +27,9 @@ jobs:
 
     - name: Install dependencies
       run: |
-        sudo apt-get update -qq
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python -m pip install jaxlib
-        python -m pip install jax
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-            
-    - name: install package
-      run: |
-        pip install .
-        pip list
+        bash scripts/install.sh
 
     - name: Notebook smoke tests
       run: |
-        pip install ipython
-        pip install nbformat
-        pip install seaborn
         bash scripts/test_notebooks.sh
 
diff --git a/scripts/test_notebooks.sh b/scripts/test_notebooks.sh
index f1f1771..e63cef5 100644
--- a/scripts/test_notebooks.sh
+++ b/scripts/test_notebooks.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 
-#!/bin/bash
+pip install ipython
+pip install nbformat
+pip install seaborn
 for nb in examples/*.ipynb; do
     echo "Running notebook smoke test on $nb"
     ipython -c "%run $nb"

From 5951f32c9565c23819047370affd20f9c3612e06 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 16:13:35 -0500
Subject: [PATCH 14/26] Disable publish to pypi for now

---
 .github/workflows/publish-to-pypi.yml | 42 +++++++++++++--------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
index 8ba346d..34d5e5b 100644
--- a/.github/workflows/publish-to-pypi.yml
+++ b/.github/workflows/publish-to-pypi.yml
@@ -27,24 +27,24 @@ jobs:
         name: python-package-distributions
         path: dist/
 
-  publish-to-pypi:
-    name: >-
-      Publish Python 🐍 distribution 📦 to PyPI
-    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
-    needs:
-    - build
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/gpax
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
-
-    steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v3
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+  # publish-to-pypi:
+  #   name: >-
+  #     Publish Python 🐍 distribution 📦 to PyPI
+  #   if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+  #   needs:
+  #   - build
+  #   runs-on: ubuntu-latest
+  #   environment:
+  #     name: pypi
+  #     url: https://pypi.org/p/gpax
+  #   permissions:
+  #     id-token: write  # IMPORTANT: mandatory for trusted publishing
+  #
+  #   steps:
+  #   - name: Download all the dists
+  #     uses: actions/download-artifact@v3
+  #     with:
+  #       name: python-package-distributions
+  #       path: dist/
+  #   - name: Publish distribution 📦 to PyPI
+  #     uses: pypa/gh-action-pypi-publish@release/v1

From 2b0003ddc68f33a52ececc4020432f7d6e94b1d8 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 16:18:47 -0500
Subject: [PATCH 15/26] Debug CI

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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c8ff29b..b2df5c1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -8,6 +8,8 @@ on:
   push:
     branches: ["master", "dev/*", mc/issue-59]
 
+jobs: 
+
   unit:
     uses: ./.github/workflows/unit.yml
 

From a257a75e3112d17ff1b95d2751c153eb2fa4e2bd Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 15 Feb 2024 17:01:16 -0500
Subject: [PATCH 16/26] Refactor CI/deploy

---
 .github/workflows/ci-deploy.yml       | 60 +++++++++++++++++++++++++++
 .github/workflows/publish-to-pypi.yml | 50 ----------------------
 2 files changed, 60 insertions(+), 50 deletions(-)
 create mode 100644 .github/workflows/ci-deploy.yml
 delete mode 100644 .github/workflows/publish-to-pypi.yml

diff --git a/.github/workflows/ci-deploy.yml b/.github/workflows/ci-deploy.yml
new file mode 100644
index 0000000..aa9c92a
--- /dev/null
+++ b/.github/workflows/ci-deploy.yml
@@ -0,0 +1,60 @@
+name: CI/Deploy
+
+on:
+  push:
+    tags: ["v*"]
+
+jobs:
+
+  unit:
+    uses: ./.github/workflows/unit.yml
+
+  notebooks:
+    uses: ./.github/workflows/notebook_smoke.yml
+
+  check_semantic_version_placeholder:
+    name: Check semantic version placeholder exists in the __init__
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v3
+
+    - name: Check lines exist
+      run: |
+        grep -x "__version__ = ...  # semantic-version-placeholder" gpax/__init__.py
+
+  build_and_publish:
+    name: Upload release to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gpax
+    permissions:
+      id-token: write
+
+    needs:
+      - check_semantic_version_placeholder
+      - unit
+      - notebooks
+
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Build and apply version
+      run: bash scripts/build_project.sh
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        # CURRENTLY USING TEST SERVER FOR NOW!!!!
+        repository-url: https://test.pypi.org/legacy/
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
deleted file mode 100644
index 34d5e5b..0000000
--- a/.github/workflows/publish-to-pypi.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
-
-on: push
-
-jobs:
-  build:
-    name: Build distribution 📦
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.x"
-    - name: Install pypa/build
-      run: >-
-        python3 -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: python3 -m build
-    - name: Store the distribution packages
-      uses: actions/upload-artifact@v3
-      with:
-        name: python-package-distributions
-        path: dist/
-
-  # publish-to-pypi:
-  #   name: >-
-  #     Publish Python 🐍 distribution 📦 to PyPI
-  #   if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
-  #   needs:
-  #   - build
-  #   runs-on: ubuntu-latest
-  #   environment:
-  #     name: pypi
-  #     url: https://pypi.org/p/gpax
-  #   permissions:
-  #     id-token: write  # IMPORTANT: mandatory for trusted publishing
-  #
-  #   steps:
-  #   - name: Download all the dists
-  #     uses: actions/download-artifact@v3
-  #     with:
-  #       name: python-package-distributions
-  #       path: dist/
-  #   - name: Publish distribution 📦 to PyPI
-  #     uses: pypa/gh-action-pypi-publish@release/v1

From a5481a92d35905da74c89ea7d96c823797f0770f Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Wed, 28 Feb 2024 17:33:14 -0500
Subject: [PATCH 17/26] Remove my version hack in favor of dunamai

---
 gpax/__init__.py          | 42 +++++++++++++++++++--------------------
 scripts/build_project.sh  |  2 --
 scripts/update_version.sh | 36 ---------------------------------
 3 files changed, 21 insertions(+), 59 deletions(-)
 delete mode 100644 scripts/update_version.sh

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 72d5ec7..53cf61a 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -1,8 +1,22 @@
 from . import acquisition, kernels, utils
 from .hypo import sample_next
-from .models import (DKL, UIGP, CoregGP, ExactGP, MeasuredNoiseGP, MultiTaskGP,
-                     VarNoiseGP, iBNN, sPM, vExactGP, vi_iBNN, viDKL, viGP,
-                     viMTDKL, viSparseGP)
+from .models import (
+    DKL,
+    UIGP,
+    CoregGP,
+    ExactGP,
+    MeasuredNoiseGP,
+    MultiTaskGP,
+    VarNoiseGP,
+    iBNN,
+    sPM,
+    vExactGP,
+    vi_iBNN,
+    viDKL,
+    viGP,
+    viMTDKL,
+    viSparseGP,
+)
 
 __all__ = [
     "utils",
@@ -27,22 +41,8 @@
     "sample_next",
 ]
 
-# DO NOT CHANGE BELOW ---------------------------------------------------------
-# ALSO DO NOT TYPE dunder version ANYWHERE ABOVE THIS
-# This is replaced at build time automatically during deployment and
-# installation. Replacing anything will mess that up and crash the entire
-# build.
-__version__ = ...  # semantic-version-placeholder
-# DO NOT CHANGE ABOVE ---------------------------------------------------------
 
-# Silly hack. Useful for local development
-if __version__ == ...:
-    try:
-        from dunamai import Version
-        version = Version.from_any_vcs()
-        __version__ = version.serialize()
-    except ImportError:
-        print("You are running a local copy of gpax (not installed via pip)")
-        print("__version__ = ...; pip install dunamai to track local version")
-        pass
-    
+import dunamai as _dunamai
+
+__version__ = _dunamai.get_version("gpax", third_choice=_dunamai.Version.from_any_vcs).serialize()
+del _dunamai
diff --git a/scripts/build_project.sh b/scripts/build_project.sh
index 0d5f6f8..5e9b2ce 100644
--- a/scripts/build_project.sh
+++ b/scripts/build_project.sh
@@ -1,6 +1,4 @@
 #!/bin/bash
 
 pip install flit~=3.7
-bash scripts/update_version.sh set
 flit build
-bash scripts/update_version.sh reset
diff --git a/scripts/update_version.sh b/scripts/update_version.sh
deleted file mode 100644
index db98116..0000000
--- a/scripts/update_version.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/bash
-
-PACKAGE_NAME="gpax"
-
-replace_version_in_init () {
-    pip install dunamai~=1.12
-    version="$(dunamai from git --style pep440 --no-metadata)"
-    dunamai check "$version" --style pep440
-    sed_command="s/...  # semantic-version-placeholder/'$version'/g"
-    if [[ "$OSTYPE" == "darwin"* ]]; then
-        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
-    else
-        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
-    fi
-    echo "__init__ version set to" "$version"
-    export _TMP_VERSION="$version"
-}
-
-reset_version_to_ellipsis () {
-    # we only grep the first instance of __version__
-    current_version=$(grep -m 1 "__version__" "$PACKAGE_NAME"/__init__.py)
-    sed_command="s/$current_version/__version__ = ...  # semantic-version-placeholder/g"
-    if [[ "$OSTYPE" == "darwin"* ]]; then
-        sed -i '' "$sed_command" "$PACKAGE_NAME"/__init__.py
-    else
-        sed -i "$sed_command" "$PACKAGE_NAME"/__init__.py
-    fi
-    echo "$current_version" "reset to placeholder"
-}
-
-
-if [ "$1" == "set" ]; then
-    replace_version_in_init
-elif [ "$1" == "reset" ]; then
-    reset_version_to_ellipsis
-fi

From fc0d70b7ddacf3e1d2b416b50e3538163cec1b2f Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Wed, 28 Feb 2024 17:33:48 -0500
Subject: [PATCH 18/26] Update pyproject with version-locked dunamai dependency

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 6091e9b..b225a6f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,6 +26,7 @@ dependencies = [
     "jax>=0.4.8",
     "numpyro>=0.11.0",
     "dm-haiku>=0.0.5",
+    "dunamai==1.19.2",
     "jaxopt", # TODO: do we want to require this?
 ]
 

From d53a25cf807447ec1d289fe2caf60c785b947fa4 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 20:11:24 -0500
Subject: [PATCH 19/26] Revise dunamai usage for dynamic versioning

---
 gpax/__init__.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 53cf61a..44c3c1e 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -18,6 +18,8 @@
     viSparseGP,
 )
 
+# WARNING: I don't think __all__ is really needed, and I'm not sure it's
+# actually accurate
 __all__ = [
     "utils",
     "kernels",
@@ -41,8 +43,11 @@
     "sample_next",
 ]
 
+try:
+    # _version.py is only written dynamically during build time
+    from gpax._version import __version__
+except ImportError:
+    import dunamai as _dunamai
 
-import dunamai as _dunamai
-
-__version__ = _dunamai.get_version("gpax", third_choice=_dunamai.Version.from_any_vcs).serialize()
-del _dunamai
+    __version__ = _dunamai.Version.from_any_vcs().serialize()
+    del _dunamai

From e19efc8021d310d061c6b80078e4919a875dfb51 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 20:37:40 -0500
Subject: [PATCH 20/26] Update ci-deploy, remove semantic version placeholder

---
 .github/workflows/ci-deploy.yml | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/ci-deploy.yml b/.github/workflows/ci-deploy.yml
index aa9c92a..e10bb6b 100644
--- a/.github/workflows/ci-deploy.yml
+++ b/.github/workflows/ci-deploy.yml
@@ -12,19 +12,6 @@ jobs:
   notebooks:
     uses: ./.github/workflows/notebook_smoke.yml
 
-  check_semantic_version_placeholder:
-    name: Check semantic version placeholder exists in the __init__
-
-    runs-on: ubuntu-latest
-
-    steps:
-
-    - uses: actions/checkout@v3
-
-    - name: Check lines exist
-      run: |
-        grep -x "__version__ = ...  # semantic-version-placeholder" gpax/__init__.py
-
   build_and_publish:
     name: Upload release to PyPI
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
@@ -36,7 +23,6 @@ jobs:
       id-token: write
 
     needs:
-      - check_semantic_version_placeholder
       - unit
       - notebooks
 
@@ -44,6 +30,8 @@ jobs:
 
     - name: Checkout
       uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
 
     - name: Set up Python 3.9
       uses: actions/setup-python@v2

From ea3b684ea9f6b84c02558550c00197829d57d0aa Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 20:38:49 -0500
Subject: [PATCH 21/26] Update build script for writing _version.py

---
 scripts/build_project.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/build_project.sh b/scripts/build_project.sh
index 5e9b2ce..e7a8fcf 100644
--- a/scripts/build_project.sh
+++ b/scripts/build_project.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
 
 pip install flit~=3.7
+echo "__version__ = '$(dunamai from any --style=pep440 --no-metadata)'" >gpax/_version.py
 flit build

From b696b9714e995c7034930f629ac5152219e0791b Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 20:41:39 -0500
Subject: [PATCH 22/26] Add _version.py file back, debugging dunamai build

---
 gpax/__init__.py | 11 ++---------
 gpax/_version.py |  7 +++++++
 2 files changed, 9 insertions(+), 9 deletions(-)
 create mode 100644 gpax/_version.py

diff --git a/gpax/__init__.py b/gpax/__init__.py
index 44c3c1e..f4a8f73 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -1,3 +1,5 @@
+from gpax._version import __version__
+
 from . import acquisition, kernels, utils
 from .hypo import sample_next
 from .models import (
@@ -42,12 +44,3 @@
     "CoregGP",
     "sample_next",
 ]
-
-try:
-    # _version.py is only written dynamically during build time
-    from gpax._version import __version__
-except ImportError:
-    import dunamai as _dunamai
-
-    __version__ = _dunamai.Version.from_any_vcs().serialize()
-    del _dunamai
diff --git a/gpax/_version.py b/gpax/_version.py
new file mode 100644
index 0000000..cabbf9c
--- /dev/null
+++ b/gpax/_version.py
@@ -0,0 +1,7 @@
+"""Version file. This is overwritten during build and will contain a static
+__version__ variable."""
+
+import dunamai as _dunamai
+
+__version__ = _dunamai.Version.from_any_vcs().serialize()
+del _dunamai

From 869a8b413347b8032ca53ebf84359d16cd8d3e48 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 22:32:30 -0500
Subject: [PATCH 23/26] Add init from main

---
 gpax/__init__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index f4a8f73..a231301 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -1,8 +1,8 @@
-from gpax._version import __version__
-
 from . import acquisition, kernels, utils
+from .__version__ import version as __version__
 from .hypo import sample_next
 from .models import (
+    BNN,
     DKL,
     UIGP,
     CoregGP,
@@ -20,8 +20,6 @@
     viSparseGP,
 )
 
-# WARNING: I don't think __all__ is really needed, and I'm not sure it's
-# actually accurate
 __all__ = [
     "utils",
     "kernels",
@@ -42,5 +40,7 @@
     "MeasuredNoiseGP",
     "viSparseGP",
     "CoregGP",
+    "BNN",
     "sample_next",
+    "__version__",
 ]

From e3cfefd204820dd4458e48763aa17d0acbbe4a73 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 22:35:48 -0500
Subject: [PATCH 24/26] Make __init__ imports explicit

---
 gpax/__init__.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gpax/__init__.py b/gpax/__init__.py
index adfafdd..132fcb4 100644
--- a/gpax/__init__.py
+++ b/gpax/__init__.py
@@ -1,8 +1,7 @@
+from gpax import acquisition, kernels, utils
 from gpax._version import __version__
-
-from . import acquisition, kernels, utils
-from .hypo import sample_next
-from .models import (
+from gpax.hypo import sample_next
+from gpax.models import (
     BNN,
     DKL,
     UIGP,

From 7d8156b89185493e2216e3aed5553674f498c59c Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Thu, 29 Feb 2024 22:43:48 -0500
Subject: [PATCH 25/26] Make the version detection slightly more flexible

Just in case someone using GPax as a dev copy does not have dunamai
installed, GPax will now gracefully fail to detect the version
and will simply use "dev" as the version name.
---
 gpax/_version.py         | 9 ++++++---
 scripts/build_project.sh | 1 +
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/gpax/_version.py b/gpax/_version.py
index cabbf9c..9807bb2 100644
--- a/gpax/_version.py
+++ b/gpax/_version.py
@@ -1,7 +1,10 @@
 """Version file. This is overwritten during build and will contain a static
 __version__ variable."""
 
-import dunamai as _dunamai
+try:
+    import dunamai as _dunamai
 
-__version__ = _dunamai.Version.from_any_vcs().serialize()
-del _dunamai
+    __version__ = _dunamai.Version.from_any_vcs().serialize()
+    del _dunamai
+except ImportError:
+    __version__ = "dev"
diff --git a/scripts/build_project.sh b/scripts/build_project.sh
index e7a8fcf..e746e62 100644
--- a/scripts/build_project.sh
+++ b/scripts/build_project.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 
 pip install flit~=3.7
+pip install dunamai==1.19.2
 echo "__version__ = '$(dunamai from any --style=pep440 --no-metadata)'" >gpax/_version.py
 flit build

From af60f98965b887a1836c00c275faccb7d414f798 Mon Sep 17 00:00:00 2001
From: Matthew Carbone <x94carbone@gmail.com>
Date: Fri, 29 Mar 2024 14:19:40 -0400
Subject: [PATCH 26/26] Modify scripts in scripts directory, remove unused
 scripts

---
 .github/workflows/ci-deploy.yml        |  2 +-
 scripts/LICENSE                        | 29 --------------------------
 scripts/README.md                      |  7 -------
 scripts/{build_project.sh => build.sh} |  0
 scripts/build_docs.sh                  | 25 ----------------------
 scripts/install.sh                     | 20 ++++--------------
 6 files changed, 5 insertions(+), 78 deletions(-)
 delete mode 100644 scripts/LICENSE
 delete mode 100644 scripts/README.md
 rename scripts/{build_project.sh => build.sh} (100%)
 delete mode 100644 scripts/build_docs.sh

diff --git a/.github/workflows/ci-deploy.yml b/.github/workflows/ci-deploy.yml
index e10bb6b..14f09d0 100644
--- a/.github/workflows/ci-deploy.yml
+++ b/.github/workflows/ci-deploy.yml
@@ -39,7 +39,7 @@ jobs:
         python-version: 3.9
 
     - name: Build and apply version
-      run: bash scripts/build_project.sh
+      run: bash scripts/build.sh
 
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/scripts/LICENSE b/scripts/LICENSE
deleted file mode 100644
index deacfc5..0000000
--- a/scripts/LICENSE
+++ /dev/null
@@ -1,29 +0,0 @@
-BSD 3-Clause License
-
-Copyright (c) 2022, Brookhaven Science Associates, LLC, Brookhaven National Laboratory
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-   may be used to endorse or promote products derived from this software
-   without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/scripts/README.md b/scripts/README.md
deleted file mode 100644
index 6f2bd92..0000000
--- a/scripts/README.md
+++ /dev/null
@@ -1,7 +0,0 @@
-# Scripts
-
-This directory contains helper scripts for GPax.
-
-- Build scripts for building the project
-- Testing script for the notebook smoke tests
-- `LICENSE` file, attributing code in this directory only to Brookhaven Science Associates (location from which the code was sourced)
diff --git a/scripts/build_project.sh b/scripts/build.sh
similarity index 100%
rename from scripts/build_project.sh
rename to scripts/build.sh
diff --git a/scripts/build_docs.sh b/scripts/build_docs.sh
deleted file mode 100644
index d42d820..0000000
--- a/scripts/build_docs.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-
-build_docs () {
-
-    if [[ "${GITHUB_ACTION_IS_RUNNING}" = 1 ]]; then
-        bash scripts/install.sh doc
-    fi
-
-    make -C docs/ html
-
-    # Helper when running on local. If not running in a GitHub Actions
-    # environment, this will attempt to open index.html with the users'
-    # default program
-    if [[ -z "${GITHUB_ACTION_IS_RUNNING}" ]]; then
-        open docs/build/html/index.html
-    fi
-    
-}
-
-pip install toml
-bash scripts/install.sh
-bash scripts/install.sh doc
-bash scripts/update_version.sh set
-build_docs
-bash scripts/update_version.sh reset
diff --git a/scripts/install.sh b/scripts/install.sh
index bbd3224..6ca7894 100644
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -1,22 +1,10 @@
 #!/bin/bash
 
-# Good stuff. The poor man's toml parser
-# https://github.com/pypa/pip/issues/8049
-# This is the analog of pip install -e ".[...]" since for whatever reason
-# it does not appear to work cleanly with pip
-
-install_test_requirements_only () {
-    python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["optional-dependencies"]["test"]))' | pip install -r /dev/stdin
-}
-
-install_requirements() {
-    python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin
-}
-
-
 pip install toml
+
 if [ "$1" = "test" ]; then
-    install_test_requirements_only
+	python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["optional-dependencies"]["test"]))' | pip install -r /dev/stdin
+
 else
-    install_requirements
+	python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin
 fi