updated pephub docs

docs/pephub/README.md

@@ -25,7 +25,7 @@ PEPhub is an open-source database, web interface, and API for sharing, retrievin
 
 - **Re-processing of GEO metadata**. The public PEPhub instance [geo namespace](https://pephub.databio.org/geo)  holds metadata from nearly 99% of the [Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/). PEPhub is updated weekly using [GEOfetch](../geofetch/README.md) to produce standardized PEP sample tables, providing a convenient API interface to GEO metadata.
 
-- **Command-line client**. You can use [PEPHubClient](developer/pephubclient/README.md) for  command-line tool and Python API, which allows authentication, download, upload of public or private projects.
+- **Command-line client**. You can use [PEPHubClient](user/pephubclient/README.md) for  command-line tool and Python API, which allows authentication, download, upload of public or private projects.
 
 - **Group PEPs with using a PEP of PEPs (POP)**. A PEP of PEPs, or simply a POP, is a type of PEP in which each row is itself a PEP. POPs allow users to organize projects into groups.
 

docs/pephub/changelog.md

@@ -2,7 +2,34 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.11.6] - 02-26-2024
+## [0.14.0] - 18-09-2024
+- Added BEDMS standardizer to PEPhub
+- Updated schema endpoints 
+- Added archive namespace endpoint
+- Fixed multiple bugs
+- A lot of UI work
+
+## [0.13.0] - 25-07-2024
+- Added schemas to the PEPhub
+- Fixed a lot of ui issues #[360](https://github.com/pepkit/pephub/pull/360)
+
+## [0.12.0] - 18-07-2024
+- Fixed CTRL+K and CTRL+S not working  #350
+- Added Project history #349
+- Fixed PEPhub won't save a table without sample_name #347
+- Fixed Moving to 'config' tab loses all unsaved changes in 'samples' tab #346
+- Fixed Pasting csv file into pephub yields error #345
+- Fixed UI is creating bogus column names when you remove existing columns. #344
+- Fixed UI invents a column name #343
+- Fixed UI issues with pasting a column header named 'sample_name' #342
+- Fixed UI glitch reloads data on save #340
+- Added Feature request: Ctrl+S to save #339
+- Fixed pephub UI removes samples in progress if you switch to a different tab without saving #338
+- Fixed pephub UI cannot delete a sample the inutitive way #337
+
+## [0.11.9] - 02-07-2024
+
+## [0.11.8] - 02-26-2024
 
 - Fix some bugs introduced as a result of the last release:
   - tag's were being removed from the URL params when selecting a project view

docs/pephub/developer/pepdbagent/changelog.md

@@ -2,26 +2,54 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.7.3] -- 2023-02-05
+## [0.11.1] -- 2024-09-04
+- Added archive table of namespaces
+- Added sort by stars
+
+## [0.11.0] -- 2024-07-24
+- Added validation schemas
+
+
+## [0.10.0] -- 2024-07-18
+- Added user delete method
+- Added project history and restoring projects
+
+
+## [0.9.0] -- 2024-06-25
+- Introduced new sample ordering with linked list [#133](https://github.com/pepkit/pepdbagent/issues/133)
+- Efficiency improvements of project update function 
+- Test restructuring 
+
+
+## [0.8.0] -- 2024-02-26
+- Fixed forking schema
+- Improved forking efficiency [#129](https://github.com/pepkit/pepdbagent/issues/129)
+- Added uploading project from dict 
+- Added get_config, get_smaples, get_subsamples methods to project module [#128](https://github.com/pepkit/pepdbagent/issues/128)
+- Fixed error handling in views API [#130](https://github.com/pepkit/pepdbagent/issues/130)
+- Added no_fail to views API 
+
+
+## [0.7.3] -- 2024-02-08
 - Fixed POP update
 - Improved error handling in views API
 - Added stats method to Namespace module
 - Updated docs
 - Added coverage
 
 
-## [0.7.2] -- 2023-02-02
+## [0.7.2] -- 2024-02-02
 - Fixed Unique Constraint in the Views
 - Fixed update project pop method
 - Fixed bug in duplicating samples
 
 
-## [0.7.1] -- 2023-01-22
+## [0.7.1] -- 2024-01-22
 - Fixed bug in Stars annotation
 - SQL efficiency improvements
 - Added sort by date in stared projects
 
-## [0.7.0] -- 2023-01-17
+## [0.7.0] -- 2024-01-17
 - Added `pop` to project table and annotation model [#107](https://github.com/pepkit/pepdbagent/issues/107)
 - Added `forked_from` feature [#73](https://github.com/pepkit/pepdbagent/issues/73)
 - Switched to pydantic2 [#105](https://github.com/pepkit/pepdbagent/issues/105)

docs/pephub/developer/pephubclient/changelog.md → docs/pephub/user/pephubclient/changelog.md

@@ -2,6 +2,17 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+
+## [0.4.4] - 2024-08-21
+### Fixed
+- Project annotation model
+
+
+## [0.4.3] - 2024-07-19
+### Updated
+- Updated models for new PEPhub API
+
+
 ## [0.4.2] - 2024-04-16
 ### Updated
 - View creation, by adding description and no_fail flag

docs/pephub/developer/pephubclient/tutorial.md → docs/pephub/user/pephubclient/tutorial.md

@@ -57,9 +57,9 @@ phc.upload(example_pep, namespace="databio", name="example", force=True)
 
 Full documentation for the Python API can be found here:
 
-- [PEPHubClient Python API](./phc_usage.md)
-- [PEPHubClient Python API - Samples](./phc_samples_usage.md)
-- [PEPHubClient Python API - Views](./phc_views_usage.md)
+- [PEPHubClient Python API](phc_usage.md)
+- [PEPHubClient Python API - Samples](phc_samples_usage.md)
+- [PEPHubClient Python API - Views](phc_views_usage.md)
 
 ----
 If you have any questions or need help, please contact us at [databio.org](https://databio.org)

mkdocs.yml

@@ -187,21 +187,21 @@ nav:
       - How to use views: pephub/user/views.md
       - PEP of PEPs (POP): pephub/user/pops.md
       - Accessing GEO metadata: pephub/user/geo.md
+      - PEPHubClient:
+        - PEPhubClient: pephub/user/pephubclient/README.md
+        - Quickstart: pephub/user/pephubclient/tutorial.md
+        - Python API: pephub/user/pephubclient/phc_usage.md
+        - Python API samples: pephub/user/pephubclient/phc_samples_usage.md
+        - Python API views: pephub/user/pephubclient/phc_views_usage.md
+        - CLI usage: pephub/user/pephubclient/cli.md
+        - Changelog: pephub/user/pephubclient/changelog.md
     - Developer guide:
       - Setup: pephub/developer/setup.md
       - Deployment: pephub/developer/deployment.md
       - Development: pephub/developer/development.md
       - Authentication: pephub/developer/authentication.md
       - Authentication Device: pephub/developer/authentication-device.md
       - Semantic search: pephub/developer/semantic-search.md
-      - PEPHubClient:
-        - PEPhubClient: pephub/developer/pephubclient/README.md
-        - Quickstart: pephub/developer/pephubclient/tutorial.md
-        - Changelog: pephub/developer/pephubclient/changelog.md
-        - Python API: pephub/developer/pephubclient/phc_usage.md
-        - Python API samples: pephub/developer/pephubclient/phc_samples_usage.md
-        - Python API views: pephub/developer/pephubclient/phc_views_usage.md
-        - CLI usage: pephub/developer/pephubclient/cli.md
       - Server settings: pephub/developer/server-settings.md
       - PEPembed:
         - PEPembed: pephub/developer/pepembed/README.md