Merge branch 'develop' into feature/2810-minimum-renku-version-property

design/003-interactive-session/003-interactive-session.md

@@ -138,7 +138,7 @@ class ISessionProvider:
         :param image_descriptor: Path to the container image descriptor file.
         :param image_name: Container image name.
         :param config: Path to the session provider specific configuration YAML.
-        :returns: a unique id for the created interactive sesssion.
+        :returns: a unique id for the created interactive session.
         """
         pass
 
@@ -184,7 +184,7 @@ class ISessionProvider:
         :param mem_request: Memory size request for the session.
         :param disk_request: Disk size request for the session.
         :param gpu_request: GPU device request for the session.
-        :returns: a unique id for the created interactive sesssion.
+        :returns: a unique id for the created interactive session.
         """
         pass
 

docs/conf.py

@@ -335,7 +335,7 @@
 
 # Autodoc configuraton.
 autoclass_content = "both"
-autodoc_mock_imports = ["persistent", "ZODB"]
+autodoc_mock_imports = ["persistent", "ZODB", "calamus"]
 autodoc_typehints = "none"
 autodoc_typehints_description_target = "documented"
 
@@ -364,3 +364,10 @@
     ("py:class", '"ValueResolver"'),
     ("py:exc", "errors.ParameterError"),
 ]
+
+nitpick_ignore_regex = [
+    ("py:class", r"calamus.*"),
+    ("py:class", r"docker.*"),
+    ("py:class", r"marshmallow.*"),
+    ("py:class", r"yaml.*"),
+]

docs/introduction.rst

@@ -24,7 +24,6 @@
    installation
    gettingstarted
    reference/index
-   api
    changes
    license
 

docs/reference/core.rst

@@ -0,0 +1,284 @@
+..
+    Copyright 2017-2022 - Swiss Data Science Center (SDSC)
+    A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+    Eidgenössische Technische Hochschule Zürich (ETHZ).
+
+    Licensed under the Apache License, Version 2.0 (the "License");
+    you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+        http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software
+    distributed under the License is distributed on an "AS IS" BASIS,
+    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    See the License for the specific language governing permissions and
+    limitations under the License.
+
+
+Core Business Logic
+===================
+
+``renku.core`` contains the business logic of renku-python. Functionality is
+split into subfolders based on topic, such as ``dataset`` or ``workflow``.
+
+Command Builder
+---------------
+
+Most renku commands require context (database/git/etc.) to be set up for them.
+The command builder pattern makes this easy by wrapping commands in factory
+methods.
+
+.. automodule:: renku.command.command_builder
+   :members:
+
+JSON-LD Schemes
+---------------
+
+Schema classes used to serialize domain models to JSON-LD.
+
+.. automodule:: renku.command.schema.activity
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.agent
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.annotation
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.calamus
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.composite_plan
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.dataset
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.entity
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.parameter
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.plan
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.command.schema.project
+   :members:
+   :show-inheritance:
+
+
+Datasets
+--------
+
+.. automodule:: renku.core.dataset.dataset
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.dataset_add
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.constant
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.context
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.datasets_provenance
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.pointer_file
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.request_model
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.tag
+   :members:
+   :show-inheritance:
+
+
+Dataset Providers
+-----------------
+
+Providers for dataset import and export
+
+.. automodule:: renku.core.dataset.providers.api
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.dataverse
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.dataverse_metadata_templates
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.doi
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.models
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.olos
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.renku
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.dataset.providers.zenodo
+   :members:
+   :show-inheritance:
+
+Workflows
+---------
+
+.. automodule:: renku.core.workflow.activity
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.workflow.concrete_execution_graph
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.workflow.plan_factory
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.workflow.types
+   :members:
+
+.. automodule:: renku.core.workflow.value_resolution
+   :members:
+   :show-inheritance:
+
+
+Sessions
+--------
+
+.. automodule:: renku.core.session.docker
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.session.session
+   :members:
+   :show-inheritance:
+
+Templates
+---------
+
+.. automodule:: renku.core.template.template
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.template.usecase
+   :members:
+   :show-inheritance:
+
+
+Errors
+------
+Errors that can be raised by ``renku.core``.
+
+.. automodule:: renku.core.errors
+   :members:
+   :show-inheritance:
+
+Utilities
+---------
+
+.. automodule:: renku.core.util.communication
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.contexts
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.datetime8601
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.doi
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.file_size
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.git
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.metadata
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.os
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.requests
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.scm
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.shacl
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.urls
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.util
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.uuid
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.core.util.yaml
+   :members:
+   :show-inheritance:
+
+Repository
+----------
+
+.. automodule:: renku.core.management.repository
+   :members:
+
+Git Internals
+-------------
+
+.. automodule:: renku.core.management.git
+   :members:
+
+.. automodule:: renku.domain_model.git
+   :members:

docs/reference/database.rst

@@ -23,5 +23,24 @@ Renku uses an internal database store in the ``.renku/metadata`` that uses a
 custom implementation of the ZODB object database, with a separate file per
 main entity.
 
+Database
+--------
+
 .. automodule:: renku.infrastructure.database
    :members:
+
+Persistent
+----------
+
+Extension of ``persistent.Persistent`` that supports immutability.
+
+.. automodule:: renku.infrastructure.persistent
+   :members:
+
+Immutable
+---------
+
+Classes to support immutability of renku models.
+
+.. automodule:: renku.infrastructure.immutable
+   :members: