Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

Sage-Bionetworks/synapser: 1.3.0

<h2>What's Changed</h2> <ul> <li>[SYNR-1515] Update to synapseclient v3.1.1 by @thomasyu888 in https://github.com/Sage-Bionetworks/synapser/pull/326</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapser/compare/1.2.0...1.3.0</p&gt

Sage-Bionetworks/synapsePythonClient: v4.0.0-rc

<h2>Highlights</h2> <ul> <li><strong>Only authentication through Personal Access Token</strong> <strong>(aka: Authentication bearer token) is supported</strong>. Review the <a href="https://python-docs.synapse.org/tutorials/authentication/">Authentication document</a> for information on setting up your usage of a Personal Access Token to authenticate with Synapse.</li> <li><strong>Date type Annotations on Synapse entities are now timezone aware</strong>. Review our <a href="https://python-docs.synapse.org/reference/annotations/">reference documentation for Annotations</a>. The <a href="https://pypi.org/project/pytz/"><code>pytz</code> package</a> is reccomended if you regularly work with data across time zones.<ul> <li>If you do not set the <code>tzinfo</code> field on a date or datetime instance we will use the timezone of the machine where the code is executing.</li> <li>If you are using the <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#annotations">Manifest TSV</a> for bulk actions on your projects you'll now see that [synapseutils.sync.syncFromSynapse][] will store dates as <code>YYYY-MM-DDTHH:MM:SSZ</code>. Review our documentation for an <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#example-manifest-file">example manifest file</a>. Additionally, if you'd like to upload an annotation in a specific timezone please make sure that it is in <a href="https://en.wikipedia.org/wiki/ISO_8601">ISO 8601 format</a>. If you do not specify a timezone it is assumed to use the timezone of the machine where the code is executing.</li> </ul> </li> <li><strong>Support for annotations with multiple values through the</strong> <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#multiple-values-of-annotations-per-key"><strong>Manifest TSV</strong></a> with the usage of a comma delimited bracket wrapped list. Any manifest files wishing to take advantage of multi-value annotations need to match this format. Examples:<ul> <li><code>["Annotation, with a comma", another annotation]</code></li> <li><code>[1,2,3]</code></li> <li><code>[2023-12-04T07:00:00Z,2000-01-01T07:00:00Z]</code></li> </ul> </li> <li>Migration and expansion of the docs site! You'll see that the look, feel, and flow of all of the information on this site has been touched. As we move forward we hope that you'll <a href="https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/7">provide the Data Processing and Engineering team feedback on areas we can improve</a>.</li> <li>Expansion of the available Python Tutorials can be found <a href="https://python-docs.synapse.org/tutorials/python_client/">starting here</a>.</li> </ul> <h2>What's Changed</h2> <ul> <li>Adding a label to the dockerfile to automatically label it for this repo by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1018</li> <li>Updates Dockerfile to Correctly Install Dependencies by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1019</li> <li>[SYNPY-1358] Correction of timestamp in annotations from manifest file by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1020</li> <li>[SYNPY-1336] Benchmarking upload with annotations by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1021</li> <li>[SYNPY-1321] Download benchmark results by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1024</li> <li>[SYNPY-1360] Migrating to mkdocstrings by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1025</li> <li>[SYNPY-1366] Add code coverage by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1029</li> <li>[SYNPY-1362] High level best practices for project structure by @thomasyu888 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1028</li> <li>[SYNPY-1371] Migrate to Google Style by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1033</li> <li>[SYNPY-1302] Replace getPermission with get_acl and add new get_permissions by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1037</li> <li>[SYNPY-1334] Revamp getting started docs by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1036</li> <li>[SYNPY-1332] Pypi deployment strategy by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1038</li> <li>[SYNPY-1370] Documentation Upgrade by @jaymedina in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li> <li>[SYNPY-1370] Minor formatting fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1039</li> <li>[SYNPY-1371] Doc fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1040</li> <li>[SYNPY-1225] Support authToken only by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1041</li> <li>[SYNPY-1392] Remove some deprecated pieces by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1043</li> <li>[Synpy 1369] Migrate to Google style by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1042</li> <li>[SYNPY-1387] Update Structure Project doc by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1044</li> <li>[SYNPY-1357] Allow multiple values in manifest TSV by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1030</li> </ul> <h2>New Contributors</h2> <ul> <li>@jaymedina made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.2.0...v4.0.0-rc</p&gt

Sage-Bionetworks/synapsePythonClient: v3.1.0-rc

<h2>What's Changed</h2> <ul> <li>[SYNPY-49] Aggregate acl based on groups by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li> <li>[SYNPY-967] deprecated memoize and added @lru_cache by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/983</li> <li>SYNPY-1285: Create pipfile by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/984</li> <li>[SYNPY-1282] Adds Type Hinting to <code>client.py</code> by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li> <li>[SYNPY-1293] Update urllib3 version dependency by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/988</li> <li>[SYNPY-1283] Replace Broken Link URL by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/989</li> <li>[SYNPY-1296] Config client error with api key or PAT by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/990</li> </ul> <h2>New Contributors</h2> <ul> <li>@BryanFauble made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li> <li>@BWMac made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.0.0...v3.1.0-rc</p&gt

Sage-Bionetworks/synapsePythonClient: v4.0.0-rc

<h2>Highlights</h2> <ul> <li><strong>Only authentication through Personal Access Token</strong> <strong>(aka: Authentication bearer token) is supported</strong>. Review the <a href="https://python-docs.synapse.org/tutorials/authentication/">Authentication document</a> for information on setting up your usage of a Personal Access Token to authenticate with Synapse.</li> <li><strong>Date type Annotations on Synapse entities are now timezone aware</strong>. Review our <a href="https://python-docs.synapse.org/reference/annotations/">reference documentation for Annotations</a>. The <a href="https://pypi.org/project/pytz/"><code>pytz</code> package</a> is reccomended if you regularly work with data across time zones.<ul> <li>If you do not set the <code>tzinfo</code> field on a date or datetime instance we will use the timezone of the machine where the code is executing.</li> <li>If you are using the <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#annotations">Manifest TSV</a> for bulk actions on your projects you'll now see that [synapseutils.sync.syncFromSynapse][] will store dates as <code>YYYY-MM-DDTHH:MM:SSZ</code>. Review our documentation for an <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#example-manifest-file">example manifest file</a>. Additionally, if you'd like to upload an annotation in a specific timezone please make sure that it is in <a href="https://en.wikipedia.org/wiki/ISO_8601">ISO 8601 format</a>. If you do not specify a timezone it is assumed to use the timezone of the machine where the code is executing.</li> </ul> </li> <li><strong>Support for annotations with multiple values through the</strong> <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#multiple-values-of-annotations-per-key"><strong>Manifest TSV</strong></a> with the usage of a comma delimited bracket wrapped list. Any manifest files wishing to take advantage of multi-value annotations need to match this format. Examples:<ul> <li><code>["Annotation, with a comma", another annotation]</code></li> <li><code>[1,2,3]</code></li> <li><code>[2023-12-04T07:00:00Z,2000-01-01T07:00:00Z]</code></li> </ul> </li> <li>Migration and expansion of the docs site! You'll see that the look, feel, and flow of all of the information on this site has been touched. As we move forward we hope that you'll <a href="https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/7">provide the Data Processing and Engineering team feedback on areas we can improve</a>.</li> <li>Expansion of the available Python Tutorials can be found <a href="https://python-docs.synapse.org/tutorials/python_client/">starting here</a>.</li> </ul> <h2>What's Changed</h2> <ul> <li>Adding a label to the dockerfile to automatically label it for this repo by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1018</li> <li>Updates Dockerfile to Correctly Install Dependencies by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1019</li> <li>[SYNPY-1358] Correction of timestamp in annotations from manifest file by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1020</li> <li>[SYNPY-1336] Benchmarking upload with annotations by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1021</li> <li>[SYNPY-1321] Download benchmark results by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1024</li> <li>[SYNPY-1360] Migrating to mkdocstrings by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1025</li> <li>[SYNPY-1366] Add code coverage by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1029</li> <li>[SYNPY-1362] High level best practices for project structure by @thomasyu888 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1028</li> <li>[SYNPY-1371] Migrate to Google Style by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1033</li> <li>[SYNPY-1302] Replace getPermission with get_acl and add new get_permissions by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1037</li> <li>[SYNPY-1334] Revamp getting started docs by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1036</li> <li>[SYNPY-1332] Pypi deployment strategy by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1038</li> <li>[SYNPY-1370] Documentation Upgrade by @jaymedina in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li> <li>[SYNPY-1370] Minor formatting fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1039</li> <li>[SYNPY-1371] Doc fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1040</li> <li>[SYNPY-1225] Support authToken only by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1041</li> <li>[SYNPY-1392] Remove some deprecated pieces by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1043</li> <li>[Synpy 1369] Migrate to Google style by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1042</li> <li>[SYNPY-1387] Update Structure Project doc by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1044</li> <li>[SYNPY-1357] Allow multiple values in manifest TSV by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1030</li> </ul> <h2>New Contributors</h2> <ul> <li>@jaymedina made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.2.0...v4.0.0-rc</p&gt

Sage-Bionetworks/synapsePythonClient: v3.1.0

<h2>What's Changed</h2> <ul> <li>[SYNPY-49] Aggregate acl based on groups by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li> <li>[SYNPY-967] deprecated memoize and added @lru_cache by @BryanFauble, @linglp in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/983</li> <li>SYNPY-1285: Create pipfile by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/984</li> <li>[SYNPY-1282] Adds Type Hinting to <code>client.py</code> by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li> <li>[SYNPY-1293] Update urllib3 version dependency by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/988</li> <li>[SYNPY-1283] Replace Broken Link URL by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/989</li> <li>[SYNPY-1296] Config client error with api key or PAT by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/990* * [SYNPY-1283] Adds Missing Trailing Space (Broken Link Fix) by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/991</li> <li>[SYNPY-1295] Adding to the credentials.rst doc by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/992</li> </ul> <h2>New Contributors</h2> <ul> <li>@BryanFauble made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li> <li>@BWMac made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.0.0...v3.1.0-rc</p&gt

Sage-Bionetworks/synapsePythonClient: v3.1.0-rc

<h2>What's Changed</h2> <ul> <li>[SYNPY-49] Aggregate acl based on groups by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li> <li>[SYNPY-967] deprecated memoize and added @lru_cache by @BryanFauble, @linglp in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/983</li> <li>SYNPY-1285: Create pipfile by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/984</li> <li>[SYNPY-1282] Adds Type Hinting to <code>client.py</code> by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li> <li>[SYNPY-1293] Update urllib3 version dependency by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/988</li> <li>[SYNPY-1283] Replace Broken Link URL by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/989</li> <li>[SYNPY-1296] Config client error with api key or PAT by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/990* * [SYNPY-1283] Adds Missing Trailing Space (Broken Link Fix) by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/991</li> <li>[SYNPY-1295] Adding to the credentials.rst doc by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/992</li> </ul> <h2>New Contributors</h2> <ul> <li>@BryanFauble made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li> <li>@BWMac made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.0.0...v3.1.0-rc</p&gt

Sage-Bionetworks/synapsePythonClient: V3.1.1-rc

<h2>What's Changed</h2> <ul> <li>[SYNPY-1298] Update annotation logic by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/995</li> <li>[SYNPY-1299] Clean up contributing.md by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/996</li> <li>[SYNPY-1299] Update contributing.md to point to service desk by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/997</li> <li>[SYNPY-1316] Fix for cache item names matching by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/998</li> <li>[SYNPY-1298] flakey integration tests by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/999</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.1.0...v3.1.1-rc</p&gt

Sage-Bionetworks/synapsePythonClient: v3.1.1

<h2>What's Changed</h2> <ul> <li>[SYNPY-1298] Update annotation logic by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/995</li> <li>[SYNPY-1299] Clean up contributing.md by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/996</li> <li>[SYNPY-1299] Update contributing.md to point to service desk by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/997</li> <li>[SYNPY-1316] Fix for cache item names matching by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/998</li> <li>[SYNPY-1298] flakey integration tests by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/999</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.1.0...v3.1.1-rc</p&gt