From 872946cf103abdc8c5da165439f94418206d0b40 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Thu, 4 Apr 2024 13:22:36 -0400
Subject: [PATCH 01/27] Setup Python package blueprint.

---
 .gitignore                              |  3 ++
 pom.xml                                 | 21 ++++++++-
 python/LICENSE                          |  1 +
 python/README.md                        | 45 +++++++++++++++++++
 python/README.rst                       |  1 +
 python/pyproject.toml                   | 58 +++++++++++++++++++++++++
 python/tests/test_top_level_elements.py |  9 ++++
 7 files changed, 136 insertions(+), 2 deletions(-)
 create mode 120000 python/LICENSE
 create mode 100644 python/README.md
 create mode 120000 python/README.rst
 create mode 100644 python/pyproject.toml
 create mode 100644 python/tests/test_top_level_elements.py

diff --git a/.gitignore b/.gitignore
index fcaeaaa8..8888f6a6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -127,6 +127,9 @@ nb-configuration.xml
 ### Python template
 !requirements.txt
 
+# We do not track the generated Protobuf files for now.
+python/**/*_pb2.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/pom.xml b/pom.xml
index a9a94d57..e2b88a65 100644
--- a/pom.xml
+++ b/pom.xml
@@ -187,16 +187,33 @@
                 </configuration>
                 <executions>
                     <execution>
+                        <id>java-cpp-js</id>
                         <goals>
                             <goal>compile</goal>
                             <goal>test-compile</goal>
-                            <goal>compile-python</goal>
-                            <goal>test-compile-python</goal>
                             <goal>compile-cpp</goal>
                             <goal>test-compile-cpp</goal>
                             <goal>compile-js</goal>
                         </goals>
                     </execution>
+                    <execution>
+                        <id>compile-python</id>
+                        <goals>
+                            <goal>compile-python</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>python/src</outputDirectory>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>compile-python-test</id>
+                        <goals>
+                            <goal>test-compile-python</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>python/tests</outputDirectory>
+                        </configuration>
+                    </execution>
                 </executions>
             </plugin>
 
diff --git a/python/LICENSE b/python/LICENSE
new file mode 120000
index 00000000..ea5b6064
--- /dev/null
+++ b/python/LICENSE
@@ -0,0 +1 @@
+../LICENSE
\ No newline at end of file
diff --git a/python/README.md b/python/README.md
new file mode 100644
index 00000000..69b4bab4
--- /dev/null
+++ b/python/README.md
@@ -0,0 +1,45 @@
+# README
+
+This folder contains the files required for building and deployment of `phenopackets` Python package.
+
+## How to release
+
+Generate the Python sources by running Maven up to `test` or more:
+
+```shell
+./mvnw test
+```
+
+Maven will run the Protobuf compiler and write the generated Python classes into `src` folder.
+
+We must do some postprocessing to maintain backward compatibility with the previous `phenopackets` versions.
+Therefore, we run a script to put all elements of Phenopacket Schema v2.0.2 into the top-level `phenopackets` package.
+
+TODO(iimpulse): implement
+
+Now is the time to run tests. Note, the tests can only be run *after* installing the package with `test` dependencies!
+Let's install the package and run the tests:
+
+```shell
+# Install the `phenopackets` with test dependencies
+python3 -m pip install .[test]
+
+# Run the tests
+pytest
+```
+
+If the tests pass, we can build and deploy the package to PyPi. 
+To do so, we will need the `build` and `twine` Python packages in the environment:
+
+```shell
+# Build
+python3 -m build
+
+# Deploy
+python3 -m twine upload dist/*
+
+# Clear the deployed files
+rm -rf dist 
+```
+
+That's it!
\ No newline at end of file
diff --git a/python/README.rst b/python/README.rst
new file mode 120000
index 00000000..89a01069
--- /dev/null
+++ b/python/README.rst
@@ -0,0 +1 @@
+../README.rst
\ No newline at end of file
diff --git a/python/pyproject.toml b/python/pyproject.toml
new file mode 100644
index 00000000..26f195c3
--- /dev/null
+++ b/python/pyproject.toml
@@ -0,0 +1,58 @@
+[build-system]
+requires = ["setuptools>=65.6.3", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "phenopackets"
+version = "2.0.2.post2"  # IMPORTANT: This must be kept in sync with `project.version` in the top-level `pom.xml`
+requires-python = ">=3.8"
+description = "Phenopacket Schema"
+readme = "README.rst"
+authors = [
+    { name = "Michael Gargano", email = "michael.gargano@jax.org" },
+    { name = "Daniel Danis", email = "daniel.gordon.danis@protonmail.com" },
+    { name = "Jules Jacobsen", email = "j.jacobsen@qmul.ac.uk" },
+    { name = "Chris Mungall", email = "cjmungall@lbl.gov" },
+    { name = "Peter Robinson", email = "peter.robinson@bih-charite.de" },
+]
+license = { file = "LICENSE" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+keywords = [
+    "Global Alliance for Genomics and Health",
+    "GA4GH Phenopacket Schema",
+    "GA4GH",
+]
+
+dependencies = [
+    # TODO: `protobuf>=3.21.7`?
+    #  Maven Central points out presence a security vulnerability in the older versions.
+    "protobuf>=3.15.0,<4.0.0",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=7.0.0, <8.0.0",
+]
+
+[project.urls]
+homepage = "https://github.com/phenopackets/phenopacket-schema"
+repository = "https://github.com/phenopackets/phenopacket-schema.git"
+documentation = "https://github.com/phenopackets/phenopacket-schema"
+bugtracker = "https://github.com/phenopackets/phenopacket-schema/issues"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests",
+]
\ No newline at end of file
diff --git a/python/tests/test_top_level_elements.py b/python/tests/test_top_level_elements.py
new file mode 100644
index 00000000..82a65365
--- /dev/null
+++ b/python/tests/test_top_level_elements.py
@@ -0,0 +1,9 @@
+
+
+class TestPhenopacket:
+
+    def test_create(self):
+        from phenopackets.schema.v2.phenopackets_pb2 import Phenopacket
+        pp = Phenopacket()
+
+        assert isinstance(pp, Phenopacket)

From c9871081c7e951ae6c91486252d1ce8eb5bb33be Mon Sep 17 00:00:00 2001
From: iimpulse <Michael.Gargano@jax.org>
Date: Thu, 4 Apr 2024 15:46:35 -0600
Subject: [PATCH 02/27] reworking for backwards compat

---
 deploy-python.sh                              | 63 ++++---------------
 pom.xml                                       |  3 -
 python/config/__init__.py                     | 13 ++++
 python/pyproject.toml                         |  6 +-
 .../test/python => python/tests}/covid19.json |  0
 {src/test/python => python/tests}/mcahs1.json |  0
 ..._top_level_elements.py => test_imports.py} |  2 +
 .../tests/test_phenopackets.py                |  8 +--
 requirements.txt                              |  2 -
 setup.py                                      | 40 ------------
 src/test/python/README.md                     | 27 --------
 src/test/python/__init__.py                   |  0
 12 files changed, 33 insertions(+), 131 deletions(-)
 create mode 100644 python/config/__init__.py
 rename {src/test/python => python/tests}/covid19.json (100%)
 rename {src/test/python => python/tests}/mcahs1.json (100%)
 rename python/tests/{test_top_level_elements.py => test_imports.py} (67%)
 rename src/test/python/phenopackets_test.py => python/tests/test_phenopackets.py (97%)
 delete mode 100644 requirements.txt
 delete mode 100644 setup.py
 delete mode 100644 src/test/python/README.md
 delete mode 100644 src/test/python/__init__.py

diff --git a/deploy-python.sh b/deploy-python.sh
index cdb7ca6f..93f1b8a4 100755
--- a/deploy-python.sh
+++ b/deploy-python.sh
@@ -1,30 +1,8 @@
-# Create Temporary Destination
-# Phenopackets folder
-TEMP_DIRECTORY=$(mktemp -d)
-echo "Building phenopacket distribution files in temporary directory at $TEMP_DIRECTORY"
-TEMP_DIRECTORY_PYTHON_MODULE="$TEMP_DIRECTORY/phenopackets"
-TEMP_DIRECTORY_TESTS_MODULE="$TEMP_DIRECTORY/tests"
-TEMP_DIRECTORY_VIRTUAL_ENV="$TEMP_DIRECTORY/phenopackets-venv"
-declare -a pyfiles=("base" "phenopackets" "biosample" "disease" "genome" "individual" "interpretation" "medical_action" "measurement" "meta_data" "pedigree" "phenotypic_feature" "vrsatile")
-# Functions
-createInitFile(){
-  echo "import pkg_resources" >> "$TEMP_DIRECTORY/phenopackets/__init__.py"
-  echo "__version__ = pkg_resources.get_distribution('phenopackets').version"   >> "$TEMP_DIRECTORY/phenopackets/__init__.py"
-  for i in "${pyfiles[@]}"
-  do
-     echo "from .${i}_pb2 import *"  >> "$TEMP_DIRECTORY/phenopackets/__init__.py"
-  done
-}
-
-replaceImports(){
-    for i in "${pyfiles[@]}"
-  do
-      sed -i 's/from phenopackets.schema.v2.core/from . /g' "$TEMP_DIRECTORY_PYTHON_MODULE/${i}_pb2.py"
-      sed -i 's/from ga4gh.vrsatile.v1/from . /g' "$TEMP_DIRECTORY_PYTHON_MODULE/${i}_pb2.py"
-      sed -i 's/from ga4gh.vrs.v1/from . /g' "$TEMP_DIRECTORY_PYTHON_MODULE/${i}_pb2.py"
-  done
-}
-
+# Build and Deploy Python Package
+DIRECTORY=./python
+echo "Building phenopacket distribution files in directory at $DIRECTORY"
+TEMP_DIRECTORY_VIRTUAL_ENV="phenopackets-venv"
+cd $DIRECTORY || { echo "Deployment FAILED. Couldn't find directory" ; exit 1; }
 createVirtualEnvironment(){
   echo "Creating Python virtual environment at ${1}"
   python3 -m venv "${1}" &> /dev/null
@@ -39,38 +17,23 @@ createVirtualEnvironment(){
   echo "Virtual environment created successfully";
 }
 
-# Create python module
-mkdir $TEMP_DIRECTORY_PYTHON_MODULE
-createInitFile
-cp ./target/generated-sources/protobuf/python/phenopackets/schema/v2/phenopackets_pb2.py $TEMP_DIRECTORY_PYTHON_MODULE
-cp ./target/generated-sources/protobuf/python/phenopackets/schema/v2/core/* $TEMP_DIRECTORY_PYTHON_MODULE
-cp ./target/generated-sources/protobuf/python/ga4gh/vrsatile/v1/vrsatile_pb2.py $TEMP_DIRECTORY_PYTHON_MODULE
-cp ./target/generated-sources/protobuf/python/ga4gh/vrs/v1/vrs_pb2.py $TEMP_DIRECTORY_PYTHON_MODULE
-replaceImports
-# Create tests module
-mkdir $TEMP_DIRECTORY_TESTS_MODULE
-cp ./src/test/python/* $TEMP_DIRECTORY_TESTS_MODULE
-# Copy Packaging files
-cp requirements.txt setup.py pom.xml LICENSE README.rst $TEMP_DIRECTORY
-
 # Create Python venv in virtual directory
 createVirtualEnvironment $TEMP_DIRECTORY_VIRTUAL_ENV
-cd $TEMP_DIRECTORY || { echo "Deployment FAILED. Couldn't cd to temp directory" ; exit 1; }
 # shellcheck disable=SC1090
 source "$TEMP_DIRECTORY_VIRTUAL_ENV/bin/activate"
-pip install -r "$TEMP_DIRECTORY/requirements.txt"
 # Dependencies for building/deploying
-python3 -m pip install setuptools wheel twine || { echo "Deployment FAILED. Failed to install python dependencies" ; exit 1; }
+python3 -m pip install build twine || { echo "Deployment FAILED. Failed to install python dependencies" ; exit 1; }
+# Rexport module definition until v3
+cp ./config/__init__.py ./src/phenopackets/
 # Test
-pip install -e .
-python3 setup.py test || { echo "Deployment FAILED. Unittest Failure" ; exit 1; }
+python3 -m pip install .[test]
+pytest || { echo "Deployment FAILED. Unittest Failure" ; exit 1; }
 # Build
-python3 setup.py sdist bdist_wheel || { echo "Deployment FAILED. Building python package" ; exit 1; }
-
+python3 -m build || { echo "Deployment FAILED. Building python package" ; exit 1; }
 # Deploy - Remove --repository testpypi flag for production.
-if [ $1 = "release-prod" ]; then
+if [ "$1" = "release-prod" ]; then
   python3 -m twine upload dist/*
-elif [ $1 = "release-test" ]; then
+elif [ "$1" = "release-test" ]; then
   python3 -m twine upload --repository testpypi dist/*
 else
   echo "Python Release was prepared successfully. No release argument provided, use one of [release-prod, release-test] to make the production/test release."
diff --git a/pom.xml b/pom.xml
index e2b88a65..95d1ca76 100644
--- a/pom.xml
+++ b/pom.xml
@@ -210,9 +210,6 @@
                         <goals>
                             <goal>test-compile-python</goal>
                         </goals>
-                        <configuration>
-                            <outputDirectory>python/tests</outputDirectory>
-                        </configuration>
                     </execution>
                 </executions>
             </plugin>
diff --git a/python/config/__init__.py b/python/config/__init__.py
new file mode 100644
index 00000000..6d243e93
--- /dev/null
+++ b/python/config/__init__.py
@@ -0,0 +1,13 @@
+from .schema.v2.core.base_pb2 import *
+from .schema.v2.core.biosample_pb2 import *
+from .schema.v2.core.disease_pb2 import *
+from .schema.v2.core.genome_pb2 import *
+from .schema.v2.core.individual_pb2 import *
+from .schema.v2.core.interpretation_pb2 import *
+from .schema.v2.core.medical_action_pb2 import *
+from .schema.v2.core.meta_data_pb2 import *
+from .schema.v2.core.pedigree_pb2 import *
+from .schema.v2.core.phenotypic_feature_pb2 import *
+from .schema.v2.phenopackets_pb2 import *
+from ga4gh.vrs.v1.vrs_pb2 import *
+from ga4gh.vrsatile.v1.vrsatile_pb2 import *
diff --git a/python/pyproject.toml b/python/pyproject.toml
index 26f195c3..7c4dd2fa 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -33,9 +33,7 @@ keywords = [
 ]
 
 dependencies = [
-    # TODO: `protobuf>=3.21.7`?
-    #  Maven Central points out presence a security vulnerability in the older versions.
-    "protobuf>=3.15.0,<4.0.0",
+    "protobuf>=3.20.2,<4.0.0",
 ]
 
 [project.optional-dependencies]
@@ -55,4 +53,4 @@ package-dir = { "" = "src" }
 [tool.pytest.ini_options]
 testpaths = [
     "tests",
-]
\ No newline at end of file
+]
diff --git a/src/test/python/covid19.json b/python/tests/covid19.json
similarity index 100%
rename from src/test/python/covid19.json
rename to python/tests/covid19.json
diff --git a/src/test/python/mcahs1.json b/python/tests/mcahs1.json
similarity index 100%
rename from src/test/python/mcahs1.json
rename to python/tests/mcahs1.json
diff --git a/python/tests/test_top_level_elements.py b/python/tests/test_imports.py
similarity index 67%
rename from python/tests/test_top_level_elements.py
rename to python/tests/test_imports.py
index 82a65365..1f4a5aa0 100644
--- a/python/tests/test_top_level_elements.py
+++ b/python/tests/test_imports.py
@@ -4,6 +4,8 @@ class TestPhenopacket:
 
     def test_create(self):
         from phenopackets.schema.v2.phenopackets_pb2 import Phenopacket
+        from phenopackets import Variation
+        from ga4gh.vrs.v1.vrs_pb2 import Variation
         pp = Phenopacket()
 
         assert isinstance(pp, Phenopacket)
diff --git a/src/test/python/phenopackets_test.py b/python/tests/test_phenopackets.py
similarity index 97%
rename from src/test/python/phenopackets_test.py
rename to python/tests/test_phenopackets.py
index fdc08796..a489917f 100644
--- a/src/test/python/phenopackets_test.py
+++ b/python/tests/test_phenopackets.py
@@ -1,13 +1,11 @@
 import os
-import unittest
 
 from google.protobuf.json_format import Parse, MessageToJson
 from google.protobuf.timestamp_pb2 import Timestamp
-
 from phenopackets import Individual, Sex, PhenotypicFeature, OntologyClass, Phenopacket
 
-
-class PhenopacketsTest(unittest.TestCase):
+# This will break when we deprecate the new stuff.
+class PhenopacketsTest:
     path = os.path.dirname(os.path.abspath(__file__))
     subject = Individual(id="Zaphod", sex="MALE", date_of_birth=Timestamp(seconds=-123456798))
     phenotypic_features = [PhenotypicFeature(type=OntologyClass(id="HG2G:00001", label="Hoopy")),
@@ -61,4 +59,4 @@ def tearDownClass(cls) -> None:
 
 
 if __name__ == '__main__':
-    unittest.main()
\ No newline at end of file
+    unittest.main()
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index c89f3b9b..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-protobuf==3.15.0
-xmltodict==0.12.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 1f0a4638..00000000
--- a/setup.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import os
-import xmltodict
-
-from setuptools import setup, find_packages
-
-path = os.path.dirname(os.path.abspath(__file__))
-
-with open(os.path.join(path, 'LICENSE')) as f:
-    LICENSE = f.read()
-
-with open(os.path.join(path, 'README.rst')) as f:
-    READ_ME = f.read()
-
-with open(os.path.join(path, 'requirements.txt')) as f:
-    REQUIREMENTS = f.read().splitlines()
-
-
-def version():
-    with open(os.path.join(path, 'pom.xml')) as f:
-        pom = xmltodict.parse(f.read())
-        return pom['project']['version']
-
-
-setup(
-      name='phenopackets',
-      version=version(),  # replace with version method
-      packages=find_packages(),
-      install_requires=REQUIREMENTS,
-      package_data={'':  ['tests/*']},
-      data_files=[('', ['requirements.txt', 'LICENSE'])],
-      test_suite="tests",
-      long_description=READ_ME,
-      long_description_content_type='text/x-rst',
-      author='Michael Gargano',
-      author_email='michael.gargano@jax.com',
-      url='https://github.com/phenopackets/phenopacket-schema',
-      description='A python implementation of phenopackets protobuf',
-      license=LICENSE,
-      keywords='phenopackets, clinical'
-      )
diff --git a/src/test/python/README.md b/src/test/python/README.md
deleted file mode 100644
index ef95d7a1..00000000
--- a/src/test/python/README.md
+++ /dev/null
@@ -1,27 +0,0 @@
-Phenopackets Python Example
-===========================
-
-Assuming this file is located in the directory `~/github/phenopacket-schema/src/test/python`
-
-```bash
-$ phenopacket_srcdir="~/github/phenopacket-schema"
-$ cd $phenopacket_srcdir
-# build the project using maven (requires Java)
-$ ./mvnw package
-# alternatively read-up on protoc
-# now setup a dir for the python virtual environment
-$ venv_dir="~/python_envs/phenopacket-schema"
-$ mkdir -p $venv_dir
-$ cd $venv_dir
-# copy the auto-generated python files to the env
-$ cp -r $phenopacket_srcdir/target/generated-sources/protobuf/python/* .
-# copy the test project files 
-$ cp $phenopacket_srcdir/src/test/python/* .
-# setup the python virtual env at `venv` in the current folder
-$ python3 -m venv venv
-$ source venv/bin/activate
-$ pip install -r $phenopacket_srcdir/requirements.txt
-$ python phenopackets_test.py
-```
-
-> the last command in the script above fails. **TODO**: resolve. 
\ No newline at end of file
diff --git a/src/test/python/__init__.py b/src/test/python/__init__.py
deleted file mode 100644
index e69de29b..00000000

From ccea6572a0cb0f62eb4cfa99f2398a5c8cf43a57 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 09:51:54 -0400
Subject: [PATCH 03/27] Add explanation to the __init__ file.

---
 python/config/__init__.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/python/config/__init__.py b/python/config/__init__.py
index 6d243e93..8e531465 100644
--- a/python/config/__init__.py
+++ b/python/config/__init__.py
@@ -1,9 +1,18 @@
+# This __init__ file should be placed into `phenopackets` package
+# for backward compatibility with `[2.0.0, 2.0.2.post1]`,
+# where we used to import Phenopacket Schema building blocks as
+# ```
+# import phenopackets as pp2
+# phenopacket = pp2.Phenopacket()
+# ```
+
 from .schema.v2.core.base_pb2 import *
 from .schema.v2.core.biosample_pb2 import *
 from .schema.v2.core.disease_pb2 import *
 from .schema.v2.core.genome_pb2 import *
 from .schema.v2.core.individual_pb2 import *
 from .schema.v2.core.interpretation_pb2 import *
+from .schema.v2.core.measurement_pb2 import *
 from .schema.v2.core.medical_action_pb2 import *
 from .schema.v2.core.meta_data_pb2 import *
 from .schema.v2.core.pedigree_pb2 import *

From d933390fc02111ca2b3067e85828fb9ddd2b2a9d Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 09:53:27 -0400
Subject: [PATCH 04/27] Finish testing.

---
 python/tests/conftest.py          |  10 +++
 python/tests/test_imports.py      | 103 ++++++++++++++++++++++++--
 python/tests/test_phenopackets.py | 118 ++++++++++++++++--------------
 3 files changed, 170 insertions(+), 61 deletions(-)
 create mode 100644 python/tests/conftest.py

diff --git a/python/tests/conftest.py b/python/tests/conftest.py
new file mode 100644
index 00000000..d27777bd
--- /dev/null
+++ b/python/tests/conftest.py
@@ -0,0 +1,10 @@
+import os
+
+import pytest
+
+
+@pytest.fixture(scope='session')
+def fpath_test_dir() -> str:
+    # When running `pytest` from the top-level Python folder (`phenopacket-schema/python`)
+    # this path will evaluate to the `tests` folder.
+    return os.path.dirname(__file__)
diff --git a/python/tests/test_imports.py b/python/tests/test_imports.py
index 1f4a5aa0..9baf1a69 100644
--- a/python/tests/test_imports.py
+++ b/python/tests/test_imports.py
@@ -1,11 +1,104 @@
+class TestImportsV202:
+    """
+    Test that the imports which we had prior `v2.0.2.post2` work.
+    """
 
+    def test_singular_import(self):
+        from phenopackets import Phenopacket
 
-class TestPhenopacket:
+        pp = Phenopacket(id='retinoblastoma.id')
 
-    def test_create(self):
+        assert isinstance(pp, Phenopacket)
+
+    def test_import_module(self):
+        import phenopackets as pp2
+
+        pp = pp2.Phenopacket(id='retinoblastoma.id')
+
+        assert isinstance(pp, pp2.Phenopacket)
+
+    def test_import_everything(self):
+        import phenopackets
+
+        pp = phenopackets.Phenopacket(id='retinoblastoma.id')
+
+        assert isinstance(pp, phenopackets.Phenopacket)
+
+    def test_import_all_sorts_of_stuff(self):
+        import phenopackets as pps
+
+        payload = (
+            pps.OntologyClass, pps.Individual, pps.PhenotypicFeature, pps.Measurement, pps.Biosample,
+            pps.Interpretation, pps.Disease, pps.MedicalAction, pps.File, pps.MetaData, pps.Family, pps.Cohort,
+        )
+
+        for clz in payload:
+            x = clz()
+            assert isinstance(x, clz)
+
+
+class TestImportsPostV202:
+    """
+    Test that the imports which we have at and after `v2.0.2.post2` work.
+    """
+
+    def test_singular_import(self):
         from phenopackets.schema.v2.phenopackets_pb2 import Phenopacket
-        from phenopackets import Variation
-        from ga4gh.vrs.v1.vrs_pb2 import Variation
-        pp = Phenopacket()
+
+        pp = Phenopacket(id='retinoblastoma.id')
 
         assert isinstance(pp, Phenopacket)
+
+    def test_import_module(self):
+        import phenopackets.schema.v2.phenopackets_pb2 as pp2
+
+        pp = pp2.Phenopacket(id='retinoblastoma.id')
+
+        assert isinstance(pp, pp2.Phenopacket)
+
+    def test_import_everything(self):
+        import phenopackets
+
+        pp = phenopackets.schema.v2.phenopackets_pb2.Phenopacket(id='retinoblastoma.id')
+
+        assert isinstance(pp, phenopackets.schema.v2.phenopackets_pb2.Phenopacket)
+
+    def test_import_v1(self):
+        from phenopackets.schema.v1.phenopackets_pb2 import Phenopacket
+
+        p = Phenopacket()
+        assert isinstance(p, Phenopacket)
+
+
+class TestImportVrsatile:
+
+    def test_singular_import(self):
+        from ga4gh.vrsatile.v1.vrsatile_pb2 import Extension
+
+        e = Extension()
+
+        assert isinstance(e, Extension)
+
+    def test_import_vrs(self):
+        import ga4gh.vrsatile.v1.vrsatile_pb2 as vrsatile
+
+        e = vrsatile.Extension()
+
+        assert isinstance(e, vrsatile.Extension)
+
+
+class TestImportVrs:
+
+    def test_singular_import(self):
+        from ga4gh.vrs.v1.vrs_pb2 import Number
+
+        number = Number()
+
+        assert isinstance(number, Number)
+
+    def test_import_vrs(self):
+        import ga4gh.vrs.v1.vrs_pb2 as vrs
+
+        n = vrs.Number()
+
+        assert isinstance(n, vrs.Number)
diff --git a/python/tests/test_phenopackets.py b/python/tests/test_phenopackets.py
index a489917f..684a1368 100644
--- a/python/tests/test_phenopackets.py
+++ b/python/tests/test_phenopackets.py
@@ -1,62 +1,68 @@
 import os
 
+import pytest
+
 from google.protobuf.json_format import Parse, MessageToJson
 from google.protobuf.timestamp_pb2 import Timestamp
 from phenopackets import Individual, Sex, PhenotypicFeature, OntologyClass, Phenopacket
 
-# This will break when we deprecate the new stuff.
-class PhenopacketsTest:
-    path = os.path.dirname(os.path.abspath(__file__))
-    subject = Individual(id="Zaphod", sex="MALE", date_of_birth=Timestamp(seconds=-123456798))
-    phenotypic_features = [PhenotypicFeature(type=OntologyClass(id="HG2G:00001", label="Hoopy")),
-                           PhenotypicFeature(type=OntologyClass(id="HG2G:00002", label="Frood"))
-                           ]
-    phenopacket = Phenopacket(id="PPKT:1", subject=subject, phenotypic_features=phenotypic_features)
-    test_json_file = "test.json"
-    def test_phenopacket_round_trip(self):
-        with open(self.test_json_file, 'w') as jsfile:
-            jsfile.write(MessageToJson(self.phenopacket))
-        with open(self.test_json_file, 'r') as jsfile:
-            phenopacket = Parse(message=Phenopacket(), text=jsfile.read())
-            self.assertEqual(phenopacket.subject.id, "Zaphod")
-            self.assertEqual(Sex.Name(phenopacket.subject.sex), "MALE")
-            for phenotypic_feature, expected_feature in zip(phenopacket.phenotypic_features, self.phenotypic_features):
-                term = phenotypic_feature.type
-                expected_term = expected_feature.type
-                self.assertEqual(term.id, expected_term.id)
-                self.assertEqual(term.label, expected_term.label)
-
-    def test_phenopacket_covid(self):
-        with(open(os.path.join(self.path,"covid19.json"), 'r')) as covid19:
-            phenopacket = Parse(message=Phenopacket(), text=covid19.read())
-            self.assertEqual("P123542", phenopacket.subject.id)
-            self.assertEqual(11, len(phenopacket.phenotypic_features))
-            self.assertEqual(2, len(phenopacket.measurements))
-            self.assertEqual("NCIT:C113237", phenopacket.measurements[0].assay.id)
-            self.assertEqual("LOINC:26474-7", phenopacket.measurements[1].assay.id)
-            self.assertEqual("MONDO:0005015", phenopacket.diseases[0].term.id)
-            self.assertEqual("cardiomyopathy", phenopacket.diseases[1].term.label)
-            self.assertNotEqual(None, phenopacket.diseases[2].onset.timestamp)
-
-    def test_phenopacket_mcahs1(self):
-        with(open(os.path.join(self.path,"mcahs1.json"), 'r')) as covid19:
-            phenopacket = Parse(message=Phenopacket(), text=covid19.read())
-            self.assertEqual("proband A", phenopacket.subject.id)
-            self.assertEqual(1, phenopacket.subject.sex)
-            self.assertEqual(3, phenopacket.interpretations[0].progress_status)
-            self.assertEqual("Bethlem myopathy 1", phenopacket.interpretations[0].diagnosis.disease.label)
-            self.assertEqual(5, phenopacket.interpretations[0].diagnosis.genomic_interpretations[0].variant_interpretation.acmg_pathogenicity_classification)
-            self.assertEqual("GENO:0000135", phenopacket.interpretations[0].diagnosis.genomic_interpretations[0].variant_interpretation.variation_descriptor.allelic_state.id)
-
-
-
-    @classmethod
-    def tearDownClass(cls) -> None:
-        try:
-            os.remove(cls.test_json_file)
-        except OSError as e:
-            print("Error: %s - %s." % (e.filename, e.strerror))
-
-
-if __name__ == '__main__':
-    unittest.main()
+
+# This will break when we deprecate the top-level import.
+class TestPhenopackets:
+
+    @pytest.fixture
+    def phenopacket(self) -> Phenopacket:
+        subject = Individual(id="Zaphod", sex="MALE", date_of_birth=Timestamp(seconds=-123456798))
+        phenotypic_features = (
+            PhenotypicFeature(type=OntologyClass(id="HG2G:00001", label="Hoopy")),
+            PhenotypicFeature(type=OntologyClass(id="HG2G:00002", label="Frood")),
+        )
+
+        return Phenopacket(id="PPKT:1", subject=subject, phenotypic_features=phenotypic_features)
+
+    def test_phenopacket_round_trip(
+        self,
+        phenopacket: Phenopacket,
+    ):
+        output: str = MessageToJson(phenopacket)
+
+        back = Parse(message=Phenopacket(), text=output)
+
+        assert back.subject.id == "Zaphod"
+        assert Sex.Name(back.subject.sex) == "MALE"
+        for phenotypic_feature, expected_feature in zip(back.phenotypic_features, phenopacket.phenotypic_features):
+            term = phenotypic_feature.type
+            expected_term = expected_feature.type
+            assert term.id == expected_term.id
+            assert term.label == expected_term.label
+
+    def test_phenopacket_covid(
+            self,
+            fpath_test_dir: str,
+    ):
+        with open(os.path.join(fpath_test_dir, "covid19.json")) as fh:
+            pp = Parse(message=Phenopacket(), text=fh.read())
+
+        assert pp.subject.id == "P123542"
+        assert len(pp.phenotypic_features) == 11
+        assert len(pp.measurements) == 2
+        assert pp.measurements[0].assay.id == "NCIT:C113237"
+        assert pp.measurements[1].assay.id == "LOINC:26474-7"
+        assert pp.diseases[0].term.id == "MONDO:0005015"
+        assert pp.diseases[1].term.label == "cardiomyopathy"
+
+        assert pp.diseases[2].onset.timestamp is not None
+
+    def test_phenopacket_mcahs1(
+            self,
+            fpath_test_dir: str,
+    ):
+        with open(os.path.join(fpath_test_dir, "mcahs1.json")) as fh:
+            pp = Parse(message=Phenopacket(), text=fh.read())
+
+        assert pp.subject.id == "proband A"
+        assert pp.subject.sex == 1
+        assert pp.interpretations[0].progress_status == 3
+        assert pp.interpretations[0].diagnosis.disease.label == "Bethlem myopathy 1"
+        assert pp.interpretations[0].diagnosis.genomic_interpretations[0].variant_interpretation.acmg_pathogenicity_classification == 5
+        assert pp.interpretations[0].diagnosis.genomic_interpretations[0].variant_interpretation.variation_descriptor.allelic_state.id == "GENO:0000135"

From 5ed24419dafdf71f91cf8d06938228086007666e Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 10:26:41 -0400
Subject: [PATCH 05/27] Revert changes to `pom.xml`, do everything in the
 deployment script.

---
 deploy-python.sh | 30 ++++++++++++++++++++++--------
 pom.xml          | 16 +---------------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/deploy-python.sh b/deploy-python.sh
index 93f1b8a4..6c89531e 100755
--- a/deploy-python.sh
+++ b/deploy-python.sh
@@ -1,7 +1,20 @@
+#!/usr/bin/env bash
+
 # Build and Deploy Python Package
+# We assume the script is ran from the top-level repository folder as ./deploy-python.sh
+
 DIRECTORY=./python
 echo "Building phenopacket distribution files in directory at $DIRECTORY"
-TEMP_DIRECTORY_VIRTUAL_ENV="phenopackets-venv"
+
+# Ensure we generated the protobuf Python files.
+./mvnw clean package
+
+# Copy the generated files into the target folder
+cp -r target/generated-sources/protobuf/python/* ${DIRECTORY}/src/
+# Add module file to re-export the v2.0.2 classes to maintain backwards compatibility
+# until we remove the classes.
+cp ${DIRECTORY}/config/__init__.py ${DIRECTORY}/src/phenopackets/
+
 cd $DIRECTORY || { echo "Deployment FAILED. Couldn't find directory" ; exit 1; }
 createVirtualEnvironment(){
   echo "Creating Python virtual environment at ${1}"
@@ -18,16 +31,17 @@ createVirtualEnvironment(){
 }
 
 # Create Python venv in virtual directory
+TEMP_DIRECTORY_VIRTUAL_ENV="phenopackets-venv"
 createVirtualEnvironment $TEMP_DIRECTORY_VIRTUAL_ENV
 # shellcheck disable=SC1090
 source "$TEMP_DIRECTORY_VIRTUAL_ENV/bin/activate"
-# Dependencies for building/deploying
-python3 -m pip install build twine || { echo "Deployment FAILED. Failed to install python dependencies" ; exit 1; }
-# Rexport module definition until v3
-cp ./config/__init__.py ./src/phenopackets/
+
 # Test
-python3 -m pip install .[test]
+python3 -m pip install ".[test]"
 pytest || { echo "Deployment FAILED. Unittest Failure" ; exit 1; }
+
+# Install dependencies for building/deploying
+python3 -m pip install build twine || { echo "Deployment FAILED. Failed to install python dependencies" ; exit 1; }
 # Build
 python3 -m build || { echo "Deployment FAILED. Building python package" ; exit 1; }
 # Deploy - Remove --repository testpypi flag for production.
@@ -39,5 +53,5 @@ else
   echo "Python Release was prepared successfully. No release argument provided, use one of [release-prod, release-test] to make the production/test release."
 fi
 
-
-
+# Clean up
+rm -rf build dist src/*
diff --git a/pom.xml b/pom.xml
index 95d1ca76..c1e1f60d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -187,28 +187,14 @@
                 </configuration>
                 <executions>
                     <execution>
-                        <id>java-cpp-js</id>
                         <goals>
                             <goal>compile</goal>
                             <goal>test-compile</goal>
                             <goal>compile-cpp</goal>
                             <goal>test-compile-cpp</goal>
-                            <goal>compile-js</goal>
-                        </goals>
-                    </execution>
-                    <execution>
-                        <id>compile-python</id>
-                        <goals>
                             <goal>compile-python</goal>
-                        </goals>
-                        <configuration>
-                            <outputDirectory>python/src</outputDirectory>
-                        </configuration>
-                    </execution>
-                    <execution>
-                        <id>compile-python-test</id>
-                        <goals>
                             <goal>test-compile-python</goal>
+                            <goal>compile-js</goal>
                         </goals>
                     </execution>
                 </executions>

From 598c3bb662b9c2ca2a1163a14ce6d93dfd045508 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 10:30:08 -0400
Subject: [PATCH 06/27] Improve clean-up.

---
 deploy-python.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/deploy-python.sh b/deploy-python.sh
index 6c89531e..5c5c99dc 100755
--- a/deploy-python.sh
+++ b/deploy-python.sh
@@ -54,4 +54,5 @@ else
 fi
 
 # Clean up
-rm -rf build dist src/*
+deactivate
+rm -rf build dist src/* ${TEMP_DIRECTORY_VIRTUAL_ENV}

From 4ed9b7629b58049457a0b29065e9a3746321a496 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 14:21:20 -0400
Subject: [PATCH 07/27] Finish merging `master` to
 `python/include-generated-files`.

---
 setup.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 setup.py

diff --git a/setup.py b/setup.py
deleted file mode 100644
index e69de29b..00000000

From 8396f1381a1225c52482414577845f565c9b3f71 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 14:22:51 -0400
Subject: [PATCH 08/27] Reorder protobuf plugin goals to the original order.

---
 pom.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 9bf70c6a..0ee8b212 100644
--- a/pom.xml
+++ b/pom.xml
@@ -190,10 +190,10 @@
                         <goals>
                             <goal>compile</goal>
                             <goal>test-compile</goal>
-                            <goal>compile-cpp</goal>
-                            <goal>test-compile-cpp</goal>
                             <goal>compile-python</goal>
                             <goal>test-compile-python</goal>
+                            <goal>compile-cpp</goal>
+                            <goal>test-compile-cpp</goal>
                             <goal>compile-js</goal>
                         </goals>
                     </execution>

From b131bb863bbb5429c5d6a64d55d564c018b8a1d3 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 5 Apr 2024 14:28:32 -0400
Subject: [PATCH 09/27] Update the python README

---
 python/README.md | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/python/README.md b/python/README.md
index 69b4bab4..f1a0c70b 100644
--- a/python/README.md
+++ b/python/README.md
@@ -10,18 +10,28 @@ Generate the Python sources by running Maven up to `test` or more:
 ./mvnw test
 ```
 
-Maven will run the Protobuf compiler and write the generated Python classes into `src` folder.
+Maven will run the Protobuf compiler and generate the Python classes.
 
-We must do some postprocessing to maintain backward compatibility with the previous `phenopackets` versions.
-Therefore, we run a script to put all elements of Phenopacket Schema v2.0.2 into the top-level `phenopackets` package.
+We copy the generated classes into the package:
 
-TODO(iimpulse): implement
+```shell
+cp -r target/generated-sources/protobuf/python/* python/src/
+```
+
+We re-export elements of `v2.0.2` schema from the top-level package to maintain the backward compatibility 
+with the previous `phenopackets` versions.
+
+```shell
+cd python
+
+cp config/__init__.py src/phenopackets/
+```
 
 Now is the time to run tests. Note, the tests can only be run *after* installing the package with `test` dependencies!
 Let's install the package and run the tests:
 
 ```shell
-# Install the `phenopackets` with test dependencies
+# Install the package with test dependencies
 python3 -m pip install .[test]
 
 # Run the tests
@@ -32,6 +42,9 @@ If the tests pass, we can build and deploy the package to PyPi.
 To do so, we will need the `build` and `twine` Python packages in the environment:
 
 ```shell
+# Install the build libraries
+python3 -m pip install build twine
+
 # Build
 python3 -m build
 

From 7c03f2dd8d4e68431c34a2608f881c6739f315d2 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Fri, 19 Apr 2024 11:59:08 -0400
Subject: [PATCH 10/27] Move the vrs/vrsatile proto files into `phenopackets`.

---
 python/config/__init__.py                                 | 4 ++--
 python/tests/test_imports.py                              | 8 ++++----
 .../phenopackets/schema/v2/core/interpretation.proto      | 2 +-
 src/main/proto/{ga4gh => phenopackets}/vrs/v1/vrs.proto   | 0
 .../{ga4gh => phenopackets}/vrsatile/v1/vrsatile.proto    | 2 +-
 src/vrs-protobuf                                          | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)
 rename src/main/proto/{ga4gh => phenopackets}/vrs/v1/vrs.proto (100%)
 rename src/main/proto/{ga4gh => phenopackets}/vrsatile/v1/vrsatile.proto (98%)

diff --git a/python/config/__init__.py b/python/config/__init__.py
index 8e531465..adc923b5 100644
--- a/python/config/__init__.py
+++ b/python/config/__init__.py
@@ -18,5 +18,5 @@
 from .schema.v2.core.pedigree_pb2 import *
 from .schema.v2.core.phenotypic_feature_pb2 import *
 from .schema.v2.phenopackets_pb2 import *
-from ga4gh.vrs.v1.vrs_pb2 import *
-from ga4gh.vrsatile.v1.vrsatile_pb2 import *
+from .vrs.v1.vrs_pb2 import *
+from .vrsatile.v1.vrsatile_pb2 import *
diff --git a/python/tests/test_imports.py b/python/tests/test_imports.py
index 9baf1a69..6f5958d6 100644
--- a/python/tests/test_imports.py
+++ b/python/tests/test_imports.py
@@ -73,14 +73,14 @@ def test_import_v1(self):
 class TestImportVrsatile:
 
     def test_singular_import(self):
-        from ga4gh.vrsatile.v1.vrsatile_pb2 import Extension
+        from phenopackets.vrsatile.v1.vrsatile_pb2 import Extension
 
         e = Extension()
 
         assert isinstance(e, Extension)
 
     def test_import_vrs(self):
-        import ga4gh.vrsatile.v1.vrsatile_pb2 as vrsatile
+        import phenopackets.vrsatile.v1.vrsatile_pb2 as vrsatile
 
         e = vrsatile.Extension()
 
@@ -90,14 +90,14 @@ def test_import_vrs(self):
 class TestImportVrs:
 
     def test_singular_import(self):
-        from ga4gh.vrs.v1.vrs_pb2 import Number
+        from phenopackets.vrs.v1.vrs_pb2 import Number
 
         number = Number()
 
         assert isinstance(number, Number)
 
     def test_import_vrs(self):
-        import ga4gh.vrs.v1.vrs_pb2 as vrs
+        import phenopackets.vrs.v1.vrs_pb2 as vrs
 
         n = vrs.Number()
 
diff --git a/src/main/proto/phenopackets/schema/v2/core/interpretation.proto b/src/main/proto/phenopackets/schema/v2/core/interpretation.proto
index 697653e7..58861f38 100644
--- a/src/main/proto/phenopackets/schema/v2/core/interpretation.proto
+++ b/src/main/proto/phenopackets/schema/v2/core/interpretation.proto
@@ -3,7 +3,7 @@ syntax = "proto3";
 package org.phenopackets.schema.v2.core;
 
 import "phenopackets/schema/v2/core/base.proto";
-import "ga4gh/vrsatile/v1/vrsatile.proto";
+import "phenopackets/vrsatile/v1/vrsatile.proto";
 
 option java_multiple_files = true;
 option java_package = "org.phenopackets.schema.v2.core";
diff --git a/src/main/proto/ga4gh/vrs/v1/vrs.proto b/src/main/proto/phenopackets/vrs/v1/vrs.proto
similarity index 100%
rename from src/main/proto/ga4gh/vrs/v1/vrs.proto
rename to src/main/proto/phenopackets/vrs/v1/vrs.proto
diff --git a/src/main/proto/ga4gh/vrsatile/v1/vrsatile.proto b/src/main/proto/phenopackets/vrsatile/v1/vrsatile.proto
similarity index 98%
rename from src/main/proto/ga4gh/vrsatile/v1/vrsatile.proto
rename to src/main/proto/phenopackets/vrsatile/v1/vrsatile.proto
index 5f56e489..c45ceb2d 100644
--- a/src/main/proto/ga4gh/vrsatile/v1/vrsatile.proto
+++ b/src/main/proto/phenopackets/vrsatile/v1/vrsatile.proto
@@ -2,7 +2,7 @@ syntax = "proto3";
 
 package org.ga4gh.vrsatile.v1;
 
-import "ga4gh/vrs/v1/vrs.proto";
+import "phenopackets/vrs/v1/vrs.proto";
 import "phenopackets/schema/v2/core/base.proto";
 
 option java_multiple_files = true;
diff --git a/src/vrs-protobuf b/src/vrs-protobuf
index d045bb0c..d3e8c390 160000
--- a/src/vrs-protobuf
+++ b/src/vrs-protobuf
@@ -1 +1 @@
-Subproject commit d045bb0c65152a0cb32177dfc21148cc13d40fbe
+Subproject commit d3e8c390f80adc7a080b7156e444bf22bd20c88e

From 2e3540ab437215e6f2717280b90a5233b5e10171 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 29 Apr 2024 21:33:20 -0400
Subject: [PATCH 11/27] Allow to import all `v2` building blocks.

---
 deploy-python.sh                    |  7 ++++---
 python/config/schema/v2/__init__.py | 18 ++++++++++++++++++
 python/tests/test_imports.py        | 24 ++++++++++++++++++++++++
 3 files changed, 46 insertions(+), 3 deletions(-)
 create mode 100644 python/config/schema/v2/__init__.py

diff --git a/deploy-python.sh b/deploy-python.sh
index 5c5c99dc..005b7de6 100755
--- a/deploy-python.sh
+++ b/deploy-python.sh
@@ -11,9 +11,9 @@ echo "Building phenopacket distribution files in directory at $DIRECTORY"
 
 # Copy the generated files into the target folder
 cp -r target/generated-sources/protobuf/python/* ${DIRECTORY}/src/
-# Add module file to re-export the v2.0.2 classes to maintain backwards compatibility
-# until we remove the classes.
-cp ${DIRECTORY}/config/__init__.py ${DIRECTORY}/src/phenopackets/
+# Add module files to re-export the v2.0.2 classes to maintain backwards compatibility,
+# and `__init__.py` to allow importing all v2 building blocks at once.
+cp -r ${DIRECTORY}/config/* ${DIRECTORY}/src/phenopackets
 
 cd $DIRECTORY || { echo "Deployment FAILED. Couldn't find directory" ; exit 1; }
 createVirtualEnvironment(){
@@ -54,5 +54,6 @@ else
 fi
 
 # Clean up
+echo "Cleaning up the build environment and the build files"
 deactivate
 rm -rf build dist src/* ${TEMP_DIRECTORY_VIRTUAL_ENV}
diff --git a/python/config/schema/v2/__init__.py b/python/config/schema/v2/__init__.py
new file mode 100644
index 00000000..f106b263
--- /dev/null
+++ b/python/config/schema/v2/__init__.py
@@ -0,0 +1,18 @@
+# The __init__ file for placing in `phenopackets.schema.v2` package
+# to allow importing all building blocks of the Phenopacket Schema v2,
+# including the VRS/VRSATILE elements.
+
+from .core.base_pb2 import *
+from .core.biosample_pb2 import *
+from .core.disease_pb2 import *
+from .core.genome_pb2 import *
+from .core.individual_pb2 import *
+from .core.interpretation_pb2 import *
+from .core.measurement_pb2 import *
+from .core.medical_action_pb2 import *
+from .core.meta_data_pb2 import *
+from .core.pedigree_pb2 import *
+from .core.phenotypic_feature_pb2 import *
+from .phenopackets_pb2 import *
+from ...vrs.v1.vrs_pb2 import *
+from ...vrsatile.v1.vrsatile_pb2 import *
diff --git a/python/tests/test_imports.py b/python/tests/test_imports.py
index 6f5958d6..cfe94c5b 100644
--- a/python/tests/test_imports.py
+++ b/python/tests/test_imports.py
@@ -69,6 +69,30 @@ def test_import_v1(self):
         p = Phenopacket()
         assert isinstance(p, Phenopacket)
 
+    def test_import_all_v2_building_blocks(self):
+        import phenopackets.schema.v2 as pps2
+
+        payload = (
+            pps2.OntologyClass, pps2.File,               # `.core.base_pb2.py`
+            pps2.Biosample,                              # `.core.biosample_pb2.py`
+            pps2.Disease,                                # `.core.disease_pb2.py`
+            # Nothing for the `.core.genome_pb2.py` file
+            pps2.Individual,                             # `.core.individual_pb2.py`
+            pps2.Interpretation,                         # `.core.interpretation_pb2.py`
+            pps2.Measurement,                            # `.core.measurement_pb2.py`
+            pps2.MedicalAction,                          # `.core.medical_action_pb2.py`
+            pps2.MetaData,                               # `.core.meta_data_pb2.py`
+            pps2.Pedigree,                               # `.core.pedigree_pb2.py`
+            pps2.PhenotypicFeature,                      # `.core.phenotypic_feature_pb2.py`
+            pps2.Cohort, pps2.Family, pps2.Phenopacket,  # `.phenopackets_pb2.py`
+            pps2.Allele,                                 # `phenopackets.vrs.v1.vrs_pb2.py`
+            pps2.VariationDescriptor,                    # `phenopackets.vrsatile.v1.vrsatile_pb2.py`
+        )
+
+        for clz in payload:
+            x = clz()
+            assert isinstance(x, clz)
+
 
 class TestImportVrsatile:
 

From e30ef0ef3cf94206a50e865e8f0e2504dfc692eb Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 29 Apr 2024 23:13:05 -0400
Subject: [PATCH 12/27] Add documentation for Python.

---
 docs/python.rst       | 140 ++++++++++++++++++++++++++++++++++++++++++
 docs/working.rst      |   1 +
 python/pyproject.toml |   2 +
 3 files changed, 143 insertions(+)
 create mode 100644 docs/python.rst

diff --git a/docs/python.rst b/docs/python.rst
new file mode 100644
index 00000000..8bd17859
--- /dev/null
+++ b/docs/python.rst
@@ -0,0 +1,140 @@
+.. _rstpython:
+
+###################################
+Working with Phenopackets in Python
+###################################
+
+Similarly to :ref:`Java <rstjava>`, the :ref:`Phenopacket Schema <rstschema>` can be considered the source of truth
+for the specification, and the JSON produced by an arbitrary implementation can be used to inter-operate
+with other services. Nevertheless, we **strongly** suggest to use the `phenopackets` library available
+from Python Package Index (PyPi) or use the Python bindings generated by Protobuf compiler from the Protobuf files.
+
+Here we provide a brief overview of the `phenopackets` library.
+
+
+Install `phenopackets` into your Python environment
+***************************************************
+
+The `phenopackets` package can be installed from PyPi by running:
+
+.. code-block:: shell
+
+    python3 -m pip install phenopackets
+
+We use `pip` to install `phenopackets` and the required libraries/dependencies.
+
+
+Create building blocks programmatically
+***************************************
+
+Let's start by importing all building blocks of Phenopacket Schema v2:
+
+>>> import phenopackets.schema.v2 as pps2
+
+Now we can access all building blocks of v2 Phenopacket Schema via `pps2` alias.
+
+For instance, we can create an :ref:`Ontology class <rstontologyclass>` that corresponds to a Human Phenotype Ontology
+term for *Spherocytosis* (`HP:0004444`):
+
+>>> spherocytosis = pps2.OntologyClass(id='HP:0004444', label='Spherocytosis')
+>>> spherocytosis # doctest: +NORMALIZE_WHITESPACE
+  id: "HP:0004444"
+  label: "Spherocytosis"
+
+All schema building blocks, including `OntologyClass`, are available under `pps2` alias, and can be created with constructors that accept key/value arguments.
+The constructors will not allow passing of arbitrary attributes:
+
+>>> pps2.OntologyClass(foo='bar')
+Traceback (most recent call last):
+  ...
+ValueError: Protocol message OntologyClass has no "foo" field.
+
+We do not have to provide all attributes at the creation time and we can set the fields sequentially
+using Python property syntax, to achieve the same outcome:
+
+>>> spherocytosis2 = pps2.OntologyClass()
+>>> spherocytosis2.id = 'HP:0004444'
+>>> spherocytosis2.label = 'Spherocytosis'
+>>> spherocytosis == spherocytosis2
+True
+
+However, setting the field values with property syntax only works for
+`singular <https://protobuf.dev/reference/python/python-generated/#singular-fields-proto3>`_ (non-message) fields,
+such as `bool`, `int`, `str`, or `float`, and the assignment will *NOT* work for message fields:
+
+>>> pf = pps2.PhenotypicFeature()
+>>> pf.type = spherocytosis
+Traceback (most recent call last):
+  ...
+AttributeError: Assignment not allowed to field "type" in protocol message object.
+
+To set a message field, we must use the `CopyFrom` function:
+
+>>> pf.type.CopyFrom(spherocytosis)
+>>> pf # doctest: +NORMALIZE_WHITESPACE
+  type {
+    id: "HP:0004444"
+    label: "Spherocytosis"
+  }
+
+Last, a repeated field can be set using list-like semantics:
+
+>>> modifiers = (
+...   pps2.OntologyClass(id='HP:0003623', label='Neonatal onset'),
+...   pps2.OntologyClass(id='HP:0011010', label='Chronic'),
+... )
+>>> pf.modifiers.extend(modifiers)
+>>> pf # doctest: +NORMALIZE_WHITESPACE
+  type {
+    id: "HP:0004444"
+    label: "Spherocytosis"
+  }
+  modifiers {
+    id: "HP:0003623"
+    label: "Neonatal onset"
+  }
+  modifiers {
+    id: "HP:0011010"
+    label: "Chronic"
+  }
+
+See `Protobuf documentation <https://protobuf.dev/reference/python/python-generated/#repeated-fields>`_
+for more info.
+
+
+Building blocks I/O
+*******************
+
+Having an instance with data, we can write the content into Protobuf's wire format:
+
+>>> binary_str = pf.SerializeToString()
+>>> binary_str
+b'\x12\x1b\n\nHP:0004444\x12\rSpherocytosis*\x1c\n\nHP:0003623\x12\x0eNeonatal onset*\x15\n\nHP:0011010\x12\x07Chronic'
+
+and get the same content back:
+
+>>> pf2 = pps2.PhenotypicFeature()
+>>> _ = pf2.ParseFromString(binary_str)
+>>> pf == pf2
+True
+
+We can also dump the content of the building block to a *JSON* string or to a `dict` with Python objects using
+`MessageToJson <https://googleapis.dev/python/protobuf/latest/google/protobuf/json_format.html#google.protobuf.json_format.MessageToJson>`_
+or `MessageToDict <https://googleapis.dev/python/protobuf/latest/google/protobuf/json_format.html#google.protobuf.json_format.MessageToDict>`_
+functions:
+
+>>> from google.protobuf.json_format import MessageToDict
+>>> json_dict = MessageToDict(pf)
+>>> json_dict
+{'type': {'id': 'HP:0004444', 'label': 'Spherocytosis'}, 'modifiers': [{'id': 'HP:0003623', 'label': 'Neonatal onset'}, {'id': 'HP:0011010', 'label': 'Chronic'}]}
+
+We complete the JSON round-trip using
+`Parse <https://googleapis.dev/python/protobuf/latest/google/protobuf/json_format.html#google.protobuf.json_format.Parse>`_
+or `ParseDict <https://googleapis.dev/python/protobuf/latest/google/protobuf/json_format.html#google.protobuf.json_format.ParseDict>`_
+functions:
+
+>>> from google.protobuf.json_format import ParseDict
+>>> pf2 = ParseDict(json_dict, pps2.PhenotypicFeature())
+>>> pf == pf2
+True
+
diff --git a/docs/working.rst b/docs/working.rst
index 3122073a..bef5e6bd 100644
--- a/docs/working.rst
+++ b/docs/working.rst
@@ -20,6 +20,7 @@ produced as part of the build (:ref:`rstjavabuild`).
    :maxdepth: 1
 
    Working with Phenopackets in Java <java>
+   Working with Phenopackets in Python <python>
    Working with Phenopackets in C++ <cpp>
 
 Security disclaimer
diff --git a/python/pyproject.toml b/python/pyproject.toml
index 7c4dd2fa..f3cab230 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -53,4 +53,6 @@ package-dir = { "" = "src" }
 [tool.pytest.ini_options]
 testpaths = [
     "tests",
+    "../docs",
 ]
+addopts = "--doctest-modules --doctest-glob=\"*.rst\""

From 71adade0a7ffc13273be57877571960a2049d9d2 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 6 May 2024 11:49:23 -0400
Subject: [PATCH 13/27] Update Maven due to `protobuf-maven-plugin`.

---
 .mvn/wrapper/maven-wrapper.properties | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties
index d26693d3..34dff68d 100644
--- a/.mvn/wrapper/maven-wrapper.properties
+++ b/.mvn/wrapper/maven-wrapper.properties
@@ -1 +1 @@
-distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.8.1/apache-maven-3.8.1-bin.zip
\ No newline at end of file
+distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.9.6/apache-maven-3.9.6-bin.zip
\ No newline at end of file

From ef66fcd8095574d67cd67c9fd28fe606661565a2 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 6 May 2024 11:50:05 -0400
Subject: [PATCH 14/27] Use `io.github.ascopes:protobuf-maven-plugin` instead
 of xolstice to enable generating Python type stubs.

---
 pom.xml | 58 +++++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 40 insertions(+), 18 deletions(-)

diff --git a/pom.xml b/pom.xml
index 0ee8b212..276dbf08 100644
--- a/pom.xml
+++ b/pom.xml
@@ -169,33 +169,55 @@
     </dependencies>
 
     <build>
-        <extensions>
-            <extension>
-                <groupId>kr.motd.maven</groupId>
-                <artifactId>os-maven-plugin</artifactId>
-                <version>1.6.0</version>
-            </extension>
-        </extensions>
         <plugins>
             <plugin>
-                <groupId>org.xolstice.maven.plugins</groupId>
+                <groupId>io.github.ascopes</groupId>
                 <artifactId>protobuf-maven-plugin</artifactId>
-                <version>0.6.1</version>
-                <extensions>true</extensions>
+                <version>1.2.1</version>
+
                 <configuration>
-                    <protocArtifact>com.google.protobuf:protoc:${protobuf.version}:exe:${os.detected.classifier}</protocArtifact>
+                    <protocVersion>${protobuf.version}</protocVersion>
+                    <sourceDirectories>
+                        <sourceDirectory>src/main/proto</sourceDirectory>
+                    </sourceDirectories>
+                    <!-- We partition the generated sources by language, a folder per language.
+                    Each language is generated in a dedicated execution.
+                    Since Java is enabled by default, we disable Java here
+                    to prevent generating Java classes into the other language's folder.
+                    -->
+                    <javaEnabled>false</javaEnabled>
                 </configuration>
                 <executions>
                     <execution>
+                        <id>generate-java</id>
+                        <goals>
+                            <goal>generate</goal>
+                        </goals>
+                        <configuration>
+                            <javaEnabled>true</javaEnabled>
+                            <outputDirectory>${project.build.directory}/generated-sources/java</outputDirectory>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>generate-python</id>
                         <goals>
-                            <goal>compile</goal>
-                            <goal>test-compile</goal>
-                            <goal>compile-python</goal>
-                            <goal>test-compile-python</goal>
-                            <goal>compile-cpp</goal>
-                            <goal>test-compile-cpp</goal>
-                            <goal>compile-js</goal>
+                            <goal>generate</goal>
                         </goals>
+                        <configuration>
+                            <pythonEnabled>true</pythonEnabled>
+                            <pythonStubsEnabled>true</pythonStubsEnabled>
+                            <outputDirectory>${project.build.directory}/generated-sources/python</outputDirectory>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>generate-cpp</id>
+                        <goals>
+                            <goal>generate</goal>
+                        </goals>
+                        <configuration>
+                            <cppEnabled>true</cppEnabled>
+                            <outputDirectory>${project.build.directory}/generated-sources/cpp</outputDirectory>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>

From 7ef57c1ed6081dc1a646e17a855940ae58c9a089 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 6 May 2024 11:50:15 -0400
Subject: [PATCH 15/27] Ignore `*.pyi` files.

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 8888f6a6..f6c4b6c3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -129,6 +129,7 @@ nb-configuration.xml
 
 # We do not track the generated Protobuf files for now.
 python/**/*_pb2.py
+python/**/*_pb2.pyi
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

From f3a9e24c84fd6d384cf7226f4b05a3376069caad Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 6 May 2024 13:07:39 -0400
Subject: [PATCH 16/27] Use Maven to manage the lifecycle of the Python
 protobuf bindings.

---
 deploy-python.sh                              | 12 +++-----
 pom.xml                                       | 30 +++++++++++--------
 .../{config => src/phenopackets}/__init__.py  |  0
 .../phenopackets}/schema/v2/__init__.py       |  0
 4 files changed, 22 insertions(+), 20 deletions(-)
 rename python/{config => src/phenopackets}/__init__.py (100%)
 rename python/{config => src/phenopackets}/schema/v2/__init__.py (100%)

diff --git a/deploy-python.sh b/deploy-python.sh
index 005b7de6..27e303ae 100755
--- a/deploy-python.sh
+++ b/deploy-python.sh
@@ -7,13 +7,7 @@ DIRECTORY=./python
 echo "Building phenopacket distribution files in directory at $DIRECTORY"
 
 # Ensure we generated the protobuf Python files.
-./mvnw clean package
-
-# Copy the generated files into the target folder
-cp -r target/generated-sources/protobuf/python/* ${DIRECTORY}/src/
-# Add module files to re-export the v2.0.2 classes to maintain backwards compatibility,
-# and `__init__.py` to allow importing all v2 building blocks at once.
-cp -r ${DIRECTORY}/config/* ${DIRECTORY}/src/phenopackets
+./mvnw clean compile
 
 cd $DIRECTORY || { echo "Deployment FAILED. Couldn't find directory" ; exit 1; }
 createVirtualEnvironment(){
@@ -56,4 +50,6 @@ fi
 # Clean up
 echo "Cleaning up the build environment and the build files"
 deactivate
-rm -rf build dist src/* ${TEMP_DIRECTORY_VIRTUAL_ENV}
+rm -rf build dist ${TEMP_DIRECTORY_VIRTUAL_ENV}
+cd ..
+./mvnw clean
diff --git a/pom.xml b/pom.xml
index 276dbf08..2ba4d789 100644
--- a/pom.xml
+++ b/pom.xml
@@ -53,6 +53,7 @@
         <protobuf.version>3.20.3</protobuf.version>
         <jackson.version>2.15.2</jackson.version>
         <hapi-fhir.version>5.7.2</hapi-fhir.version>
+        <python.src>${project.basedir}/python/src</python.src>
     </properties>
 
     <distributionManagement>
@@ -195,7 +196,6 @@
                         </goals>
                         <configuration>
                             <javaEnabled>true</javaEnabled>
-                            <outputDirectory>${project.build.directory}/generated-sources/java</outputDirectory>
                         </configuration>
                     </execution>
                     <execution>
@@ -206,17 +206,7 @@
                         <configuration>
                             <pythonEnabled>true</pythonEnabled>
                             <pythonStubsEnabled>true</pythonStubsEnabled>
-                            <outputDirectory>${project.build.directory}/generated-sources/python</outputDirectory>
-                        </configuration>
-                    </execution>
-                    <execution>
-                        <id>generate-cpp</id>
-                        <goals>
-                            <goal>generate</goal>
-                        </goals>
-                        <configuration>
-                            <cppEnabled>true</cppEnabled>
-                            <outputDirectory>${project.build.directory}/generated-sources/cpp</outputDirectory>
+                            <outputDirectory>${python.src}</outputDirectory>
                         </configuration>
                     </execution>
                 </executions>
@@ -274,6 +264,22 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-clean-plugin</artifactId>
+                <version>3.3.2</version>
+                <configuration>
+                    <filesets>
+                        <fileset>
+                            <!-- Delete the generated *.py and *.pyi files except of the manually added re-exports. -->
+                            <directory>${python.src}</directory>
+                            <excludes>
+                                <exclude>**/__init__.py</exclude>
+                            </excludes>
+                        </fileset>
+                    </filesets>
+                </configuration>
+            </plugin>
         </plugins>
     </build>
 </project>
diff --git a/python/config/__init__.py b/python/src/phenopackets/__init__.py
similarity index 100%
rename from python/config/__init__.py
rename to python/src/phenopackets/__init__.py
diff --git a/python/config/schema/v2/__init__.py b/python/src/phenopackets/schema/v2/__init__.py
similarity index 100%
rename from python/config/schema/v2/__init__.py
rename to python/src/phenopackets/schema/v2/__init__.py

From 527bc724f531cdce19d1429b845b36f0728c16ad Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:04:00 +0200
Subject: [PATCH 17/27] Ignore VS Code files.

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index f6c4b6c3..4617a216 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,6 +25,9 @@ buildNumber.properties
 # Avoid ignoring Maven wrapper jar file (.jar files are usually ignored)
 !maven-wrapper.jar
 
+# VS Code files
+.vscode/
+
 ### JetBrains template
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio
 

From 60010d1bcab1b84bd43d92b28ca48c39d76e677d Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:04:52 +0200
Subject: [PATCH 18/27] Upgrade protobuf plugin, embed protobuf source files in
 JAR.

---
 pom.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 2ba4d789..bf8d7d40 100644
--- a/pom.xml
+++ b/pom.xml
@@ -174,7 +174,7 @@
             <plugin>
                 <groupId>io.github.ascopes</groupId>
                 <artifactId>protobuf-maven-plugin</artifactId>
-                <version>1.2.1</version>
+                <version>2.2.3</version>
 
                 <configuration>
                     <protocVersion>${protobuf.version}</protocVersion>
@@ -187,6 +187,7 @@
                     to prevent generating Java classes into the other language's folder.
                     -->
                     <javaEnabled>false</javaEnabled>
+                    <embedSourcesInClassOutputs>true</embedSourcesInClassOutputs>
                 </configuration>
                 <executions>
                     <execution>

From 6ce7f95fc6b8edf22e9e8eb4d3a338ee8829bf29 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:08:36 +0200
Subject: [PATCH 19/27] Add CI to run Python tests.

---
 .github/workflows/python.yml | 45 ++++++++++++++++++++++++++++++++++++
 docs/python.rst              |  2 +-
 2 files changed, 46 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/python.yml

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
new file mode 100644
index 00000000..b025f255
--- /dev/null
+++ b/.github/workflows/python.yml
@@ -0,0 +1,45 @@
+# This workflow will generate a Python protobuf bindings and type stubs with Maven and run Python tests.
+
+name: Python CI with Maven and Pytest
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  workflow_dispatch:
+  
+jobs:
+  run-python-ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+  
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+      
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      
+      - name: Build with Maven
+        run: ./mvnw -B package -DskipTests # we run tests elsewhere
+      
+      - name: Install Python bindings
+        run: |
+          cd python && python3 -m pip install .[test]
+      
+      - name: Run Python tests
+        run: |
+          pytest
+  
\ No newline at end of file
diff --git a/docs/python.rst b/docs/python.rst
index 8bd17859..a54316f3 100644
--- a/docs/python.rst
+++ b/docs/python.rst
@@ -66,7 +66,7 @@ such as `bool`, `int`, `str`, or `float`, and the assignment will *NOT* work for
 >>> pf.type = spherocytosis
 Traceback (most recent call last):
   ...
-AttributeError: Assignment not allowed to field "type" in protocol message object.
+AttributeError: Assignment not allowed to composite field "type" in protocol message object.
 
 To set a message field, we must use the `CopyFrom` function:
 

From 976bfe352469f6033d45b390dc8c7d854490a733 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:35:52 +0200
Subject: [PATCH 20/27] Checkout `d045bb0` in vrs-protobuf.

---
 src/vrs-protobuf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/vrs-protobuf b/src/vrs-protobuf
index d3e8c390..d045bb0c 160000
--- a/src/vrs-protobuf
+++ b/src/vrs-protobuf
@@ -1 +1 @@
-Subproject commit d3e8c390f80adc7a080b7156e444bf22bd20c88e
+Subproject commit d045bb0c65152a0cb32177dfc21148cc13d40fbe

From b0cc680a06fdf227939014089457b08bce7928d0 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:41:43 +0200
Subject: [PATCH 21/27] Only collect Python tests for now.

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index b025f255..cb68c630 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -41,5 +41,5 @@ jobs:
       
       - name: Run Python tests
         run: |
-          pytest
+          pytest --collect-only
   
\ No newline at end of file

From b1aa56d0b1a84d92196ba59faaad669336891ae8 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:44:17 +0200
Subject: [PATCH 22/27] Change to `python` before running Python tests.

---
 .github/workflows/python.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index cb68c630..6d6efa0a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -32,7 +32,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       
-      - name: Build with Maven
+      - name: Generate Python bindings with Maven
         run: ./mvnw -B package -DskipTests # we run tests elsewhere
       
       - name: Install Python bindings
@@ -41,5 +41,6 @@ jobs:
       
       - name: Run Python tests
         run: |
-          pytest --collect-only
+          pwd
+          cd python && pytest --collect-only
   
\ No newline at end of file

From 9cf2f7e84be9c9ed544cb3f77c8e6d9525ca2282 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:45:44 +0200
Subject: [PATCH 23/27] Now run the Python tests.

---
 .github/workflows/python.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 6d6efa0a..7727824f 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -41,6 +41,5 @@ jobs:
       
       - name: Run Python tests
         run: |
-          pwd
-          cd python && pytest --collect-only
+          cd python && pytest
   
\ No newline at end of file

From 732764bd84f992f98da84a86edaa293dd02fbfe8 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:50:37 +0200
Subject: [PATCH 24/27] The exception message differs across Python versions.
 However, we do not care as long as we get the expected exception type.

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

diff --git a/docs/python.rst b/docs/python.rst
index a54316f3..0b0b8cea 100644
--- a/docs/python.rst
+++ b/docs/python.rst
@@ -63,7 +63,7 @@ However, setting the field values with property syntax only works for
 such as `bool`, `int`, `str`, or `float`, and the assignment will *NOT* work for message fields:
 
 >>> pf = pps2.PhenotypicFeature()
->>> pf.type = spherocytosis
+>>> pf.type = spherocytosis # doctest: +IGNORE_EXCEPTION_DETAIL
 Traceback (most recent call last):
   ...
 AttributeError: Assignment not allowed to composite field "type" in protocol message object.

From 4c6fdd71524e2024a47fd24de13656a745ffa2cd Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:53:44 +0200
Subject: [PATCH 25/27] Update `maven-dependency-submission-action`.

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

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
index fcc9a00a..14e335ee 100644
--- a/.github/workflows/maven.yml
+++ b/.github/workflows/maven.yml
@@ -34,4 +34,4 @@ jobs:
 
     # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
     - name: Update dependency graph
-      uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6
+      uses: advanced-security/maven-dependency-submission-action@v4.0.3

From 95a47c12d0918fea9f5f2003f25f62d2c2fc8198 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 12:56:03 +0200
Subject: [PATCH 26/27] Revert the `maven-dependency-submission-action`
 version.

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

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
index 14e335ee..fcc9a00a 100644
--- a/.github/workflows/maven.yml
+++ b/.github/workflows/maven.yml
@@ -34,4 +34,4 @@ jobs:
 
     # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
     - name: Update dependency graph
-      uses: advanced-security/maven-dependency-submission-action@v4.0.3
+      uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6

From 7372760bb5d668695065f6bf13ace93bfb15085f Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Mon, 1 Jul 2024 14:04:19 +0200
Subject: [PATCH 27/27] Mention the limitations of VRS objects in Phenopacket
 Schema v2.

---
 docs/variant.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/variant.rst b/docs/variant.rst
index e29a88c8..cf2d3a92 100644
--- a/docs/variant.rst
+++ b/docs/variant.rst
@@ -109,6 +109,13 @@ Variation
 be it a genomic, transcript or protein variation. VRS also provides mechanisms for representing haplotypes and systemic
 variation such as Copy Number Variants (CNVs).
 
+.. note::
+
+  When introduced in Phenopacket Schema v2, a protobuf version of VRS (github.com/ga4gh/vrs-protobuf) 
+  was derived from the source VRS representation in JSON schema and used for phenopackets.
+  The `vrs-protobuf` message structure is losslessly transformable but syntactically distinct 
+  from the native VRS JSON schema.
+
 .. _rstvcfrecord:
 
 VcfRecord