Update FUNDING.yml

updated broken links in component and description table.  Added hyperlink to digital biomarker variable guide on github page.

.github/FUNDING.yml

@@ -0,0 +1,13 @@
+# These are supported funding model platforms
+
+github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+patreon: # Replace with a single Patreon username
+open_collective: opendbm
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: AiCure/open_dbm
+otechie: # Replace with a single Otechie username
+lfx_crowdfunding: # Replace with a single LFX Crowdfunding project-name e.g., cloud-foundry
+custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

.github/workflows/open_dbm-build-checking.yml

@@ -114,6 +114,7 @@ jobs:
 #        wsl --list
 #    - name: Set up QEMU
 #      uses: docker/setup-qemu-action@v2
+#
 #    - name: Set up Docker Buildx
 #      uses: docker/setup-buildx-action@v2
 #    - name: Login to Docker Hub

.github/workflows/open_dbm-code-checking.yml

@@ -124,7 +124,7 @@ jobs:
         ls -lart
         pip install pytest coverage
         coverage run -m pytest
-        coverage report -mi --fail-under=30 --skip-covered
+        coverage report -mi --fail-under=80 --skip-covered
     - name: Update shield TEST status only for branch push master
       if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' && always() }}
       run: |

CONTRIBUTING.md

@@ -5,6 +5,7 @@ Please visit [openDBM](https://aicure.com/opendbm/) page if you have not seen it
 ## What you should know
 
 - Read [code of conduct](https://github.com/AiCure/open_dbm/blob/master/CODE_OF_CONDUCT.md).
+- Read [issues](https://github.com/AiCure/open_dbm/blob/master/ISSUES.md).
 - Read [License](https://github.com/AiCure/open_dbm/blob/master/license.txt).
 - Agree to contribute code under openDBM(GPL v3.0).
 - Before adding new feature/algorithmn make sure it's not patented.

README.md

@@ -28,7 +28,7 @@ OpenDBM is a software package that allows for calculation of digital
 biomarkers of health and functioning from video or audio of an individual’s 
 behavior. It integrates existing tools for behavioral measurements such as
 facial activity, voice, speech, and movement into a single package for measurement 
-of overall behavior.
+of overall behavior.  Checkout the OpenDBM [**digital biomarker variables**](https://aicure.github.io/open_dbm/docs/biomaker-variables) and [list of scientific publications](https://docs.google.com/spreadsheets/d/1p22VDBA6A7md5335oqAtzSV3NUs0fFb7aufQH2cqhyQ/edit#gid=0)
 
 # More About OpenDBM
 
@@ -36,10 +36,10 @@ At a modular level, OpenDBM is a library that consists of the following componen
 
 | Component | Description |
 | ---- | --- |
-| [**Facial**](https://aicure.github.io/open_dbm/docs/category/api/facial) | An OpenDBM module to get facial attributes |
+| [**Facial**](https://aicure.github.io/open_dbm/api/facial-activity-api) | An OpenDBM module to get facial attributes |
-| [**Movement**](https://aicure.github.io/open_dbm/docs/category/api/movement) | An OpenDBM module to get movement attributes |
+| [**Movement**](https://aicure.github.io/open_dbm/api/movement-api) | An OpenDBM module to get movement attributes |
-| [**Acoustic**](https://aicure.github.io/open_dbm/docs/category/api/acoustic) | An OpenDBM module to get acoustic attributes  |
+| [**Verbal Acoustic**](https://aicure.github.io/open_dbm/api/verbal-acoustics-api) | An OpenDBM module to get verbal acoustic attributes  |
-| [**Audio**](https://aicure.github.io/open_dbm/docs/category/api/audio) | An OpenDBM module to get audio attributes |
+| [**Speech & Language**](https://aicure.github.io/open_dbm/api/speech-api) | An OpenDBM module to get speech & language attributes |
 
 Usually, OpenDBM is used for:
 
@@ -122,18 +122,21 @@ landmark.to_dataframe() # convert results as pandas dataframe
 
 For more in-depth tutorials about OpenDBM, you can check out:
 
--   [Introduction to OpenDBM](https://aicure.github.io/open_dbm/docs/intro)
+-   [Introduction to OpenDBM](https://aicure.github.io/open_dbm/docs/getting-started)
--   [Advance Guide](https://aicure.github.io/open_dbm/docs/advance)
+-   [Digital Biomarker Variables](https://aicure.github.io/open_dbm/docs/biomaker-variables)
--   [API Documentation](https://aicure.github.io/open_dbm/docs/category/api)
+-   [API Documentation](https://aicure.github.io/open_dbm/api/api-doc)
+-   [Contribution Guide](https://aicure.github.io/open_dbm/extras/extras)
 
 <div align="right">
 <a href="#table-of-contents">Back to TOC ☝️</a>
 </div>
 
 # ⭐️ More resources
--   [Our wiki](https://github.com/AiCure/open_dbm/wiki)
+-   [OpenDBM Github Pages](https://aicure.github.io/open_dbm/)
--   [OpenDBM 2.0 Documentation](https://docs.google.com/document/d/1O6OUSY9FHFCZfpIWu3Kgg0Q_dyp073xjjQ2K3viEffU/edit#heading=h.rxr2y5t62mwa)
+-   [OpenDBM 2.0 Documentation](https://docs.google.com/document/d/1zek5fBvOZ_OwPYpsD6pso4u1N4K-ZuTO7j9ycHJSB-s/edit?usp=sharing)
 -   [AiCure page](https://aicure.com/opendbm/)
+-   [Submit to the list of publications](https://docs.google.com/forms/d/e/1FAIpQLScVDFF8Kkl_C4iq6N6-T6m4JwwPmFIt-Wwa70DgL4L4eGLaeA/viewform?vc=0&c=0&w=1&flr=0)
+-   [Sign up to join the list serve](https://docs.google.com/forms/d/e/1FAIpQLScKUCdYdK9UTd569IuF3O8Q2A9fXuMJ5z9wXbX4r5yzcwfphQ/viewform?fbzx=-1747756377554914236&pli=1)
 
 <div align="right">
 <a href="#table-of-contents">Back to TOC ☝️</a>
@@ -144,7 +147,7 @@ OpenDBM is published under the GNU AGPL 3.0 license.
 
 
 # ⭐️ People
-OpenDBM was developed by Anzar Abbas and Vijay Yadav, alongside Vidya Koesmahargyo and Isaac Galatzer-Levy, from within the Research and Development department at AiCure––a health tech startup in New York. It was made open source in October 2020. You can contact us at opendbm@aicure.com.
+OpenDBM is maintained by the Clinical Data Science Team (including Andre Paredes, Director of OpenDBM) at AiCure. Current development and maintenance build on the efforts of Anzar Abbas and Vijay Yadav, alongside Vidya Koesmahargyo and Isaac Galatzer-Levy.  OpenDBM was made open source in October 2020. Email the community at opendbm@aicure.com.
 
 <div align="right">
 <a href="#table-of-contents">Back to TOC ☝️</a>
@@ -153,4 +156,3 @@ OpenDBM was developed by Anzar Abbas and Vijay Yadav, alongside Vidya Koesmaharg
 
 
 
-

docs/docs/mac-linux-usage.md

@@ -1,5 +1,5 @@
 ---
-id: opendbm-docker-usage
+id: mac-linux-usage
 title: Mac / Linux Usage
 ---
 

docs/docs/opendbm-docker-usage.md

@@ -1,6 +1,6 @@
 ---
 id: opendbm-docker-usage
-title: Docker Usage
+title: Docker Mac-Linux Usage
 ---
 
 ## Mac / Linux

docs/docs/windows-usage.md

@@ -1,6 +1,6 @@
 ---
 id: windows-usage
-title: Windows Usage
+title: Docker Windows Usage
 ---
 
 import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem';

docs/website/api/api-doc.md

@@ -1,6 +1,6 @@
 ---
 id: api-doc
-title: OpendDBM API
+title: OpenDBM API
 ---
 
 This section give an overview of OpenDBM APi methods and functions. It is not a requirement to be familiar with all materials to be effective with OpenDBM. You can still benefit from this section as it will give you insights into how we manage things to give added values to this repository.

images/badges/code_coverage.svg

@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="126" height="20" role="img" aria-label="code:coverage: 81%"><title>code:coverage: 81%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="126" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="91" height="20" fill="#555"/><rect x="91" width="35" height="20" fill="#97ca00"/><rect width="126" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="465" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="810">code:coverage</text><text x="465" y="140" transform="scale(.1)" fill="#fff" textLength="810">code:coverage</text><text aria-hidden="true" x="1075" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="250">81%</text><text x="1075" y="140" transform="scale(.1)" fill="#fff" textLength="250">81%</text></g></svg>
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="126" height="20" role="img" aria-label="code:coverage: 83%"><title>code:coverage: 83%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="126" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="91" height="20" fill="#555"/><rect x="91" width="35" height="20" fill="#97ca00"/><rect width="126" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="465" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="810">code:coverage</text><text x="465" y="140" transform="scale(.1)" fill="#fff" textLength="810">code:coverage</text><text aria-hidden="true" x="1075" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="250">83%</text><text x="1075" y="140" transform="scale(.1)" fill="#fff" textLength="250">83%</text></g></svg>

images/badges/macos_status.svg

@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="133" height="20" role="img" aria-label="macos:build: failed"><title>macos:build: failed</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="133" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="94" height="20" fill="#555"/><rect x="94" width="39" height="20" fill="#e05d44"/><rect width="133" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><image x="5" y="3" width="14" height="14" xlink:href="data:image/svg+xml;base64,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"/><text aria-hidden="true" x="565" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="670">macos:build</text><text x="565" y="140" transform="scale(.1)" fill="#fff" textLength="670">macos:build</text><text aria-hidden="true" x="1125" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="290">failed</text><text x="1125" y="140" transform="scale(.1)" fill="#fff" textLength="290">failed</text></g></svg>
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="143" height="20" role="img" aria-label="macos:build: passed"><title>macos:build: passed</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="143" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="94" height="20" fill="#555"/><rect x="94" width="49" height="20" fill="#97ca00"/><rect width="143" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><image x="5" y="3" width="14" height="14" xlink:href="data:image/svg+xml;base64,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"/><text aria-hidden="true" x="565" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="670">macos:build</text><text x="565" y="140" transform="scale(.1)" fill="#fff" textLength="670">macos:build</text><text aria-hidden="true" x="1175" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="390">passed</text><text x="1175" y="140" transform="scale(.1)" fill="#fff" textLength="390">passed</text></g></svg>

images/badges/test_status.svg

@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="108" height="20" role="img" aria-label="test:status: failed"><title>test:status: failed</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="108" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="69" height="20" fill="#555"/><rect x="69" width="39" height="20" fill="#e05d44"/><rect width="108" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="355" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="590">test:status</text><text x="355" y="140" transform="scale(.1)" fill="#fff" textLength="590">test:status</text><text aria-hidden="true" x="875" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="290">failed</text><text x="875" y="140" transform="scale(.1)" fill="#fff" textLength="290">failed</text></g></svg>
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="118" height="20" role="img" aria-label="test:status: passed"><title>test:status: passed</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="118" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="69" height="20" fill="#555"/><rect x="69" width="49" height="20" fill="#97ca00"/><rect width="118" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="355" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="590">test:status</text><text x="355" y="140" transform="scale(.1)" fill="#fff" textLength="590">test:status</text><text aria-hidden="true" x="925" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="390">passed</text><text x="925" y="140" transform="scale(.1)" fill="#fff" textLength="390">passed</text></g></svg>

opendbm/api_lib/util.py

@@ -131,8 +131,8 @@ def docker_command_dec(fn):
 
     def inner(*args, **kwargs):
         wsl_cmd, path = wsllize((args[1]))
-
+        openface_repo = "opendbmteam/dbm-openface"
-        check_docker_model_exist(wsl_cmd, "dbm-openface")
+        check_docker_model_exist(wsl_cmd, openface_repo)
 
         create_docker = wsl_cmd + [
             "docker",
@@ -140,7 +140,7 @@ def docker_command_dec(fn):
             "-ti",
             "--name",
             "dbm_container",
-            "dbm-openface",
+            openface_repo,
             "bash",
         ]
 

setup.py

@@ -1,4 +1,3 @@
-# Copyright (C) 2012-2022 james jameson
 
 
 if __name__ == "__main__":