From af8f4dc0bac5498755a4eab0a930385468dc962b Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 12:08:44 -0700
Subject: [PATCH 01/10] Add GH action for pytest and lint

---
 .github/workflows/qc.yml | 77 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 .github/workflows/qc.yml

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
new file mode 100644
index 00000000..fe18190d
--- /dev/null
+++ b/.github/workflows/qc.yml
@@ -0,0 +1,77 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://github.com/snok/install-poetry#workflows-and-tips
+
+name: Build and test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.9', '3.10' ]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4.3.0
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install tox
+      - name: Check code quality with flake8
+        run: tox -e flake8
+
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, windows-latest ]
+        python-version: [ "3.9", "3.10" ]
+        exclude:
+          - os: windows-latest
+            python-version: "3.9"
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      #          install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3.1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+
+      - name: Install dependencies
+        # if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      - name: Generate coverage results
+        run: |
+          poetry run pip install -U pytest
+          poetry run coverage run -p -m pytest tests/
+          poetry run coverage combine
+          poetry run coverage xml
+          poetry run coverage report -m
+

From 119d7595b8d020078858d518f3239830729c2825 Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 12:12:02 -0700
Subject: [PATCH 02/10] Continue on lint error (at least for now)

---
 .github/workflows/qc.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index fe18190d..4cc1d9a9 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -13,6 +13,7 @@ on:
 jobs:
   lint:
     runs-on: ubuntu-latest
+    continue-on-error: true  # This line allows the job to continue even if errors occur
     strategy:
       matrix:
         python-version: [ '3.9', '3.10' ]

From b10ee8b4d843836d8f6a412ae2626d682fcf9568 Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 12:14:10 -0700
Subject: [PATCH 03/10] Comment out linting for now

---
 .github/workflows/qc.yml | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index 4cc1d9a9..80ffa66d 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -11,23 +11,23 @@ on:
     branches: [ main ]
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    continue-on-error: true  # This line allows the job to continue even if errors occur
-    strategy:
-      matrix:
-        python-version: [ '3.9', '3.10' ]
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4.3.0
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          pip install tox
-      - name: Check code quality with flake8
-        run: tox -e flake8
+#  lint:
+#    runs-on: ubuntu-latest
+#    continue-on-error: true  # This line allows the job to continue even if errors occur
+#    strategy:
+#      matrix:
+#        python-version: [ '3.9', '3.10' ]
+#    steps:
+#      - uses: actions/checkout@v3
+#      - name: Set up Python ${{ matrix.python-version }}
+#        uses: actions/setup-python@v4.3.0
+#        with:
+#          python-version: ${{ matrix.python-version }}
+#      - name: Install dependencies
+#        run: |
+#          pip install tox
+#      - name: Check code quality with flake8
+#        run: tox -e flake8
 
   test:
     strategy:

From a6f26c8f6836b50dcf50f7143add3c1e9e92d6cb Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 12:32:04 -0700
Subject: [PATCH 04/10] Run doctests

---
 .github/workflows/qc.yml | 21 +++------------------
 tox.ini                  | 11 +++++++++--
 2 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index 80ffa66d..1927e312 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -38,36 +38,22 @@ jobs:
         exclude:
           - os: windows-latest
             python-version: "3.9"
-
     runs-on: ${{ matrix.os }}
-
     steps:
-
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
-      - name: Check out repository
-        uses: actions/checkout@v3
-
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
-
-      #----------------------------------------------
-      #          install & configure poetry
-      #----------------------------------------------
       - name: Install Poetry
         uses: snok/install-poetry@v1.3.1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-
-
       - name: Install dependencies
-        # if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install --no-interaction --no-root
-
+      - name: Run Doctests
+        run: poetry run tox -e doctest
       - name: Generate coverage results
         run: |
           poetry run pip install -U pytest
@@ -75,4 +61,3 @@ jobs:
           poetry run coverage combine
           poetry run coverage xml
           poetry run coverage report -m
-
diff --git a/tox.ini b/tox.ini
index 3cd151dd..703d07f2 100644
--- a/tox.ini
+++ b/tox.ini
@@ -44,6 +44,13 @@ commands =
     flake8 src/ tests/
 description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).
 
+[testenv:doctest]
+deps =
+    pytest
+    pytest-cov
+commands =
+    pytest --doctest-modules src/
+
 #########################
 # Flake8 Configuration  #
 # (.flake8)             #
@@ -66,7 +73,7 @@ ignore =
     #S603 # subprocess call - check for execution of untrusted input.
     S607 # Starting a process with a partial executable path ["open" in both cases]
     #S608 # Possible SQL injection vector through string-based query construction.
-    #B024 # StreamingWriter is an abstract base class, but it has no abstract methods. 
+    #B024 # StreamingWriter is an abstract base class, but it has no abstract methods.
          # Remember to use @abstractmethod, @abstractclassmethod and/or @abstractproperty decorators.
     #B027 # empty method in an abstract base class, but has no abstract decorator. Consider adding @abstractmethod
     #N803 # math-oriented classes can ignore this (e.g. hypergeometric.py)
@@ -80,4 +87,4 @@ application-import-names =
     pheval_template
     tests
 # exclude =
-#    datamodels   ## datamodels are auto-generated
\ No newline at end of file
+#    datamodels   ## datamodels are auto-generated

From 0e4a9793abf7246d3c7265cbcdec51836516cb64 Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 12:35:29 -0700
Subject: [PATCH 05/10] Add tox as dev dependency

---
 .gitignore     |  1 +
 poetry.lock    | 95 +++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |  3 ++
 3 files changed, 98 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index d0097e95..d1858f8b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ data/*
 prompts/*
 inputdir
 outputdir
+.openai_cache.db
diff --git a/poetry.lock b/poetry.lock
index e2b54ab0..96322476 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -899,6 +899,17 @@ files = [
 graph = ["objgraph (>=1.7.2)"]
 profile = ["gprof2dot (>=2022.7.29)"]
 
+[[package]]
+name = "distlib"
+version = "0.3.8"
+description = "Distribution utilities"
+optional = false
+python-versions = "*"
+files = [
+    {file = "distlib-0.3.8-py2.py3-none-any.whl", hash = "sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784"},
+    {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"},
+]
+
 [[package]]
 name = "distro"
 version = "1.9.0"
@@ -1030,6 +1041,22 @@ files = [
     {file = "fastobo-0.12.3.tar.gz", hash = "sha256:f375932a24b078706797eb9296740f2d2e6987a34309bda7c9f235aba1d74217"},
 ]
 
+[[package]]
+name = "filelock"
+version = "3.14.0"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "filelock-3.14.0-py3-none-any.whl", hash = "sha256:43339835842f110ca7ae60f1e1c160714c5a6afd15a2873419ab185334975c0f"},
+    {file = "filelock-3.14.0.tar.gz", hash = "sha256:6ea72da3be9b8c82afd3edcf99f2fffbb5076335a5ae4d03248bb5b6c3eae78a"},
+]
+
+[package.extras]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
+
 [[package]]
 name = "flask"
 version = "3.0.3"
@@ -3810,6 +3837,25 @@ files = [
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyproject-api"
+version = "1.6.1"
+description = "API to interact with the python pyproject.toml based projects"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pyproject_api-1.6.1-py3-none-any.whl", hash = "sha256:4c0116d60476b0786c88692cf4e325a9814965e2469c5998b830bba16b183675"},
+    {file = "pyproject_api-1.6.1.tar.gz", hash = "sha256:1817dc018adc0d1ff9ca1ed8c60e1623d5aaca40814b953af14a9cf9a5cae538"},
+]
+
+[package.dependencies]
+packaging = ">=23.1"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+docs = ["furo (>=2023.8.19)", "sphinx (<7.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "setuptools (>=68.1.2)", "wheel (>=0.41.2)"]
+
 [[package]]
 name = "pyreadline3"
 version = "3.4.1"
@@ -5221,6 +5267,33 @@ files = [
     {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"},
 ]
 
+[[package]]
+name = "tox"
+version = "4.15.0"
+description = "tox is a generic virtualenv management and test command line tool"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "tox-4.15.0-py3-none-any.whl", hash = "sha256:300055f335d855b2ab1b12c5802de7f62a36d4fd53f30bd2835f6a201dda46ea"},
+    {file = "tox-4.15.0.tar.gz", hash = "sha256:7a0beeef166fbe566f54f795b4906c31b428eddafc0102ac00d20998dd1933f6"},
+]
+
+[package.dependencies]
+cachetools = ">=5.3.2"
+chardet = ">=5.2"
+colorama = ">=0.4.6"
+filelock = ">=3.13.1"
+packaging = ">=23.2"
+platformdirs = ">=4.1"
+pluggy = ">=1.3"
+pyproject-api = ">=1.6.1"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+virtualenv = ">=20.25"
+
+[package.extras]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-argparse-cli (>=1.11.1)", "sphinx-autodoc-typehints (>=1.25.2)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.11)"]
+testing = ["build[virtualenv] (>=1.0.3)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.2)", "devpi-process (>=1)", "diff-cover (>=8.0.2)", "distlib (>=0.3.8)", "flaky (>=3.7)", "hatch-vcs (>=0.4)", "hatchling (>=1.21)", "psutil (>=5.9.7)", "pytest (>=7.4.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-xdist (>=3.5)", "re-assert (>=1.1)", "time-machine (>=2.13)", "wheel (>=0.42)"]
+
 [[package]]
 name = "tqdm"
 version = "4.66.4"
@@ -5392,6 +5465,26 @@ files = [
     {file = "validators-0.28.1.tar.gz", hash = "sha256:5ac88e7916c3405f0ce38ac2ac82a477fcf4d90dbbeddd04c8193171fc17f7dc"},
 ]
 
+[[package]]
+name = "virtualenv"
+version = "20.26.1"
+description = "Virtual Python Environment builder"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"},
+    {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"},
+]
+
+[package.dependencies]
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<5"
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+
 [[package]]
 name = "watchdog"
 version = "4.0.0"
@@ -5678,4 +5771,4 @@ multidict = ">=4.0"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "7455db7666722ff6f052784f841c8efa02edbe54f6611e1f1c372d6539dd08a6"
+content-hash = "4c8d2fd260442ce45507714fcab1917d8c606349b5860edb99f1cab1208790bc"
diff --git a/pyproject.toml b/pyproject.toml
index ad6bbc7e..d79ebdac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,6 +23,9 @@ coverage = "^6.5.0"
 # https://github.com/monarch-initiative/ontogpt.git branch multilanguage_gpt
 ontogpt = {git = "https://github.com/monarch-initiative/ontogpt.git", branch = "multilanguage_gpt"}
 
+[tool.poetry.group.dev.dependencies]
+tox = "^4.15.0"
+
 [tool.pytest.ini_options]
 pythonpath = [
     "src"

From ace82010227fdc30675463f67bc9751e31a16ba3 Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 13:00:20 -0700
Subject: [PATCH 06/10] Pin to OntoGPT main (not multilanguage_gpt)

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d79ebdac..f9da07d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,8 +20,7 @@ pytest = "^7.1.2"
 pylint = "^2.15.6"
 pycodestyle = "^2.10.0"
 coverage = "^6.5.0"
-# https://github.com/monarch-initiative/ontogpt.git branch multilanguage_gpt
-ontogpt = {git = "https://github.com/monarch-initiative/ontogpt.git", branch = "multilanguage_gpt"}
+ontogpt = {git = "https://github.com/monarch-initiative/ontogpt.git", branch = "main"}
 
 [tool.poetry.group.dev.dependencies]
 tox = "^4.15.0"

From 0a836a467c6ebda7f697ab767bf697ea9fb5be3d Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 13:28:02 -0700
Subject: [PATCH 07/10] Change GH action to use python >= 3.10

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

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index 1927e312..d4d06f31 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -34,10 +34,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ "3.9", "3.10" ]
+        python-version: [ "3.10" ]
         exclude:
           - os: windows-latest
-            python-version: "3.9"
+            python-version: "3.10"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v3

From 889b526fdea57c7282eb96c81b567497f34d133b Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 13:30:55 -0700
Subject: [PATCH 08/10] poetry lock --no-update

---
 poetry.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 96322476..3466af55 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -3064,8 +3064,8 @@ web = ["Jinja2 (>=3.1.2)", "fastapi (>=0.88.0)", "uvicorn (>=0.20.0)"]
 [package.source]
 type = "git"
 url = "https://github.com/monarch-initiative/ontogpt.git"
-reference = "multilanguage_gpt"
-resolved_reference = "4613da4f2c6c7c4e33c0c29496910ba16a2afbd6"
+reference = "main"
+resolved_reference = "3f755df0398afc44c60a301b3a3d903438d7cccf"
 
 [[package]]
 name = "ontoportal-client"
@@ -5771,4 +5771,4 @@ multidict = ">=4.0"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "4c8d2fd260442ce45507714fcab1917d8c606349b5860edb99f1cab1208790bc"
+content-hash = "076dee9f738378d4aae0d0985054f15ade28c227b6b75c31d91847e3c70c390b"

From f862be9730f31e26d8cbddbcd5198a9d9a0b29ac Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 13:37:01 -0700
Subject: [PATCH 09/10] poetry install in tox.ini before doctest

---
 tox.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tox.ini b/tox.ini
index 703d07f2..018b539c 100644
--- a/tox.ini
+++ b/tox.ini
@@ -48,6 +48,8 @@ description = Run the flake8 tool with several plugins (bandit, docstrings, impo
 deps =
     pytest
     pytest-cov
+commands_pre =
+    poetry install
 commands =
     pytest --doctest-modules src/
 

From fd6f6581dd8a0766abb19c380a42b9ab86cd5f44 Mon Sep 17 00:00:00 2001
From: Justin Reese <justaddcoffee@gmail.com>
Date: Fri, 10 May 2024 13:41:36 -0700
Subject: [PATCH 10/10] Allow poetry

---
 tox.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tox.ini b/tox.ini
index 018b539c..27f05cb7 100644
--- a/tox.ini
+++ b/tox.ini
@@ -48,6 +48,8 @@ description = Run the flake8 tool with several plugins (bandit, docstrings, impo
 deps =
     pytest
     pytest-cov
+isolated_build = true
+allowlist_externals = poetry
 commands_pre =
     poetry install
 commands =