Merge pull request #908 from CitrineInformatics/release/v3.0

Bump to 3.0

Author: anoto-moniz

.github/workflows/pr-checks.yml

@@ -0,0 +1,45 @@
+name: PR Checks
+
+on:
+  pull_request:
+    branches:
+      - main
+      - 'release/**'
+
+jobs:
+  check-version:
+    name: Check version bumped
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Initialize the environment
+        uses: ./.github/actions/initialize
+      - name: Check version
+        run: python scripts/validate_version_bump.py
+  linting:
+    name: Run linting with flake8
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Initialize the environment
+        uses: ./.github/actions/initialize
+      - name: Lint the src/ directory
+        run: flake8 src/
+  check-deprecated:
+    name: Find code marked for removal in this version
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Initialize the environment
+        uses: ./.github/actions/initialize
+      - name: Deprecated check
+        run: derp src/ src/citrine/__version__.py
+  check-docs:
+    name: Check docs for warnings
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Initialize the environment
+        uses: ./.github/actions/initialize
+      - name: Build Docs
+        run: make -C docs/ html SPHINXOPTS='-W --keep-going'

.github/workflows/pr-tests.yml

@@ -2,40 +2,15 @@ name: PR Tests
 
 on:
   pull_request:
-    branches:    
+    branches:
       - main
+      - 'release/**'
 
 jobs:
-  check-version:
-    name: Check version bumped
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Initialize the environment
-        uses: ./.github/actions/initialize
-      - name: Check version
-        run: python scripts/validate_version_bump.py
-  linting:
-    name: Run linting with flake8
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Initialize the environment
-        uses: ./.github/actions/initialize
-      - name: Lint the src/ directory
-        run: flake8 src/
-  check-deprecated:
-    name: Find code marked for removal in this version
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Initialize the environment
-        uses: ./.github/actions/initialize
-      - name: Deprecated check
-        run: derp src/ src/citrine/__version__.py
   run-tests:
     name: Execute unit tests
     runs-on: ubuntu-latest
+    continue-on-error: true
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]

CONTRIBUTING.md

@@ -21,11 +21,11 @@ Clone from github:
 git clone [email protected]:CitrineInformatics/citrine-python
 ```
 
-Create a virtual environment using Python >= 3.7.
+Create a virtual environment using Python >= 3.8.
 One option is to use conda, but it is not required.
 
 ```bash
-conda create -n <environment_name> python=3.7
+conda create -n <environment_name> python=3.8
 conda activate <environment_name>
 ```
 

docs/source/FAQ/index.rst

@@ -6,4 +6,5 @@ FAQ
     :maxdepth: 2
 
     prohibited_data_patterns
-    team_management_migration
+    team_management_migration
+    v3_migration

docs/source/FAQ/v3_migration.rst

@@ -0,0 +1,158 @@
+================
+Migrating to 3.0
+================
+
+Summary
+=======
+
+The newest major release of citrine-python cleans accumulated deprecations as we evolve the Citrine
+platform. The intent is to focus users as we aim to reduce confusion by providing a single way to
+accomplish each of your tasks.
+
+Keep in mind that you can keep using 2.x until you're ready to upgrade. But until you do, you won't
+get any new features or bug fixes.
+
+Goals
+-----
+
+The intent of this guide is not to itemize every piece of code removed. The easiest way to
+determine what you'll need to change is to upgrade citrine to the latest 2.x release (2.42.2), run
+your scripts, and take note of the deprecation warnings. Whenever possible, those warnings will
+direct you on how to modify your code such that it will continue to function as desired upon
+upgrading to citrine-python 3.x.
+
+This guide seeks to give a high-level overview of those changes, naming some of the categories of
+elements no longer supported and what action to take, as well as some of the more consequential
+individual changes.
+
+Versions / Runtimes
+===================
+
+The following library versions and Python versions are no longer supported.
+
+Versions < 2.26.1
+-----------------
+
+The citrine-python SDK is a client for the Citrine platform. As such, we will occasionally need to
+make upgrades to the platform which will break old versions of the SDK.
+
+At some point after the release of 3.0, we will be making platform upgrades which will change the
+way clients must interact with Search Spaces. So if you're using any version of citrine prior to
+2.26.1 (released on June 28, 2023), and you're interacting with Search Spaces (e.g. through
+:py:attr:`project.design_spaces <citrine.resources.project.Project.design_spaces>`), your code will
+break. Please upgrade to the latest 2.x release, or to 3.0, to avoid this issue. If this poses any
+problems for you, please notify your customer contact so we can work with you.
+
+Python 3.7
+----------
+
+Official upstream support for Python 3.7 by the Python Software Foundation ended in June 2023. As
+such, we no longer support its use, and may begin using language features which are not backwards
+compatable with it. Upgrade to at least Python 3.8, keeping in mind
+`their migration guide <https://docs.python.org/3.8/whatsnew/3.8.html>`_.
+
+Features
+========
+
+The following features are no longer supported.
+
+Branch ID
+---------
+
+Previously, branch references were inconsistent. Some used a unique "branch ID", and others the
+"root ID". This was further complicated by the web app only ever showing the "root ID". The reason
+has to do with the platform implementation, but resulted in a confusing user experience.
+
+Beginning in 3.0, that "branch ID" is hidden from users. Instead, the SDK will always present the
+branch's root ID and version, akin to
+:py:class:`Predictor <citrine.informatics.predictors.graph_predictor.GraphPredictor>` ID and
+version. To access branches, you'll just use that root ID, and optionally the version: omitting the
+version will grab the most recent version, which will almost always be what you want.
+
+status_info
+-----------
+
+We have completed moving all our assets which previously used :code:`status_info` (such as but not
+limited to :py:class:`~citrine.informatics.predictors.predictor.Predictor` and
+:py:class:`~citrine.informatics.workflows.design_workflow.DesignWorkflow`) to use
+:code:`status_detail`. These objects contain richer information, such as log level and (optionally)
+error codes, along with the message.
+
+DesignSpace.archive and DesignSpace.restore
+-------------------------------------------
+
+In the past, archiving a Search Space required updating it, which carried the risk of accidental
+modification. Since 2.26.1, we've supported a separate
+:py:meth:`~citrine.resources.design_space.DesignSpaceCollection.archive` and 
+:py:meth:`~citrine.resources.design_space.DesignSpaceCollection.restore` call. So we no longer
+support archiving via :py:meth:`~citrine.resources.design_space.DesignSpaceCollection.update`.
+
+citrine.builders
+----------------
+
+This package contained a handful of utilities which were by all accounts unused, and better suited
+to live outside citrine-python, anyways.
+
+formulation_descriptor parameters
+---------------------------------
+
+In many cases, the Citrine platform will generate an appropriate formulation descriptor on your
+behalf. For example, when creating a
+:py:class:`~citrine.informatics.predictors.simple_mixture_predictor.SimpleMixturePredictor` or
+:py:class:`~citrine.informatics.data_sources.GemTableDataSource`. In such cases, you can no longer
+specify a formulation descriptor.
+
+:py:attr:`project.modules <citrine.resources.project.ProjectCollection.modules>`
+--------------------------------------------------------------------------------
+
+This was the remnant of the old Citrine platform, before we began to specialize our assets. For
+over a year, it has only returned Search Spaces, for which you should be using
+:py:meth:`project.design_spaces <citrine.resources.project.ProjectCollection.design_spaces>`. As
+such, both it and :code:`citrine.resources.modules` were dropped.
+
+Dehydrated Search Spaces
+------------------------
+
+This is a feature from the early days of the platform. It hasn't been supported for quite some time
+due to lack of use and complexity of support. But mechanisms for it were still present in
+citrine-python, allowing users to specify subspaces by ID. Fully dropping support completes its
+removal.
+
+Process File Protocol
+---------------------
+
+This refers to the old method of getting data on the platform using :code:`Dataset.files.process`.
+It's been supplanted by :py:meth:`~citrine.resources.file_link.FileCollection.ingest`, rendering
+:code:`process` and the whole :code:`citrine.resources.job` module irrelevant.
+
+convert_to_graph and convert_and_update
+---------------------------------------
+
+:code:`SimpleMLPredictor` was a very old type of AI Model which hasn't been supported by the
+platform in a long time. As such, these methods to convert them into the equivalent
+:py:class:`~citrine.informatics.predictors.graph_predictor.GraphPredictor` are no longer needed. If
+you think you still use a :code:`SimpleMLPredictor`, please reach out to your customer contact so we can
+work with you to convert it.
+
+:py:meth:`~citrine.seeding.find_or_create.find_or_create_project` requires a team ID
+------------------------------------------------------------------------------------
+
+In mid-2022, the platform introduced teams, which are collections of projects. As such, starting
+with 3.0, :py:meth:`~citrine.seeding.find_or_create.find_or_create_project` can only operate on a
+:py:class:`~citrine.resources.project.ProjectCollection` which includes a team ID. That is, instead
+of passing :py:attr:`citrine.projects <citrine.citrine.Citrine.projects>`, you most likely want to
+pass :py:attr:`team.projects <citrine.resources.team.Team.projects>`.
+
+Ingredient Ratio Constraint bases are now sets
+----------------------------------------------
+
+They were initially implemented as Python dictionaries to allow for flexibility. But as we evolved
+their usage on the platform, we found we only needed the list of ingredients/labels. To allow
+migration while preserving the old behavior, we added
+:py:meth:`~citrine.informatics.constraints.ingredient_ratio_constraint.IngredientRatioConstraint.basis_ingredient_names`
+and
+:py:meth:`~citrine.informatics.constraints.ingredient_ratio_constraint.IngredientRatioConstraint.basis_label_names`.
+Note that
+once you've upgraded to 3.0, you'll be prompted to move back to
+:py:meth:`~citrine.informatics.constraints.ingredient_ratio_constraint.IngredientRatioConstraint.basis_ingredients` and
+:py:meth:`~citrine.informatics.constraints.ingredient_ratio_constraint.IngredientRatioConstraint.basis_labels`.

docs/source/conf.py

@@ -13,7 +13,7 @@
 import citrine
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../src'))
+sys.path.insert(0, os.path.abspath('../../src/citrine'))
 
 
 # -- Project information -----------------------------------------------------
@@ -44,7 +44,7 @@
 # build.
 #
 # See: https://github.com/sphinx-contrib/apidoc
-apidoc_module_dir = '../../src'
+apidoc_module_dir = '../../src/citrine'
 apidoc_output_dir = 'reference'
 apidoc_excluded_paths = ['tests']
 apidoc_separate_modules = True

docs/source/data_extraction.rst

@@ -8,7 +8,7 @@ A GEM Table is defined on a set of material histories, and the rows in the resul
 Columns correspond to data about the material histories, such as the temperature measured in a kiln used at a specific manufacturing step.
 
 Defining rows and columns
-------------------------
+-------------------------
 
 A Row object describes a mapping from a list of Datasets to rows of a table by selecting a set of Material Histories.
 Each Material History corresponds to exactly one row, though the Material Histories may overlap such that the same objects contribute data to multiple rows.
@@ -327,4 +327,4 @@ are compatible with each type of descriptor:
 - :class:`~citrine.informatics.descriptors.ChemicalFormulaDescriptor`: values of type :class:`~gemd.entity.EmpiricalFormula`,
   or values of type :class:`~gemd.entity.NominalComposition` when **all** quantity keys are valid atomic symbols
 - :class:`~citrine.informatics.descriptors.FormulationDescriptor`: all values extracted by ingredient quantity, identifier, and label variables
-  are used to represent the formulation
+  are used to represent the formulation

docs/source/getting_started/datasets.rst

@@ -74,7 +74,7 @@ Assume you have a "band gaps project" with known id, ``band_gaps_project_id``, a
    
 
 Dataset Access, Sharing, and Transfer
-------------------------------------
+-------------------------------------
 
 When a Dataset is created on the Citrine Platform, only members of the project in which it was created can see it and interact with it.
 If a Dataset is made public, it (and its entire contents) can be retrieved by any user using any project.

docs/source/index.rst

@@ -8,7 +8,7 @@ Welcome to the Citrine Python client documentation!
 
 This site documents the Python SDK for the Citrine Platform.
 It provides utilities to upload and manage data and design materials using Sequential Learning.
-See the :ref:`getting started <getting-started>` guide for a high-level introduction.
+See the :ref:`getting started <ai-engine-getting-started>` guide for a high-level introduction.
 The :ref:`workflows <workflows>` section documents how to configure and run artificial intelligence (AI) workflows for materials research and development.
 
 Installation
@@ -24,7 +24,7 @@ or a specific version can be installed, for example:
 
 .. code::
 
-  pip install citrine==1.0.0
+  pip install citrine==3.0.0
 
 
 Table of Contents
@@ -41,6 +41,7 @@ Table of Contents
    formulations_example
    molecular_generation
    FAQ/index
+   API Reference <reference/modules>
 
 Indices and tables
 ==================