Add Checkout action to Docker workflow (#209)

.github/workflows/docker.yaml

@@ -6,25 +6,24 @@ jobs:
   main:
     runs-on: ubuntu-20.04
     steps:
-      -
-        name: Set up QEMU
+      - name: Set up QEMU
         uses: docker/setup-qemu-action@v1
-      -
-        name: Set up Docker Buildx
+      - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v1
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v1 
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build and push
         id: docker_build
         uses: docker/build-push-action@v2
         with:
+          context: .
+          file: ./Dockerfile
           push: true
           tags: moshiresearch/rapids:latest
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

docs/change-log.md

@@ -1,47 +1,68 @@
 # Change Log
+
 ## v1.9.2
-- Add mutation script to fix character encoding of application_name column in phone applications foreground data  
+
+- Add mutation script to fix character encoding of application_name column in phone applications foreground data
 - Fix discrepancies between computed episode and event features in PHONE_APPLICATIONS_FOREGROUND RAPIDS provider
 - Upgrade cli, lifecycle, lubridate, pillar, and vctrs R packages
 - Fix bug that scrambled the column order of resampled episodes when processng multiple time zones and some data fell outside those timezone periods
 - Resolve column specification warning messages produced by readable_datetime.R script
+- Add Checkout action to Docker workflow for solving an issue that can cause Build & Push action to fail
+
 ## v1.9.1
+
 - It fixes a library conflict that broke RAPIDS installation
+
 ## v1.9.0
+
 - Upgrade generics, stringi, Hmisc, ellipsis, glue, rlang, tibble, and vctrs packages
 - Optimize memory usage in readable_datetime.R script
 - Fix the bug of missing local_segment column in FITBIT_SLEEP_SUMMARY RAPIDS provider
 - Add TYPING_SESSION_DURATION parameter for typing sessions detection to PHONE_KEYBOARD RAPIDS provider
 - Add steps volatility features
 - Add tests for steps volatility features
+
 ## v1.8.0
+
 - Add data stream for AWARE Micro server
 - Fix the NA bug in PHONE_LOCATIONS BARNETT provider
 - Fix the bug of data type for call_duration field
 - Fix the index bug of heatmap_sensors_per_minute_per_time_segment
+
 ## v1.7.1
+
 - Update docs for Git Flow section
 - Update RAPIDS paper information
+
 ## v1.7.0
+
 - Add firststeptime and laststeptime features to FITBIT_STEPS_INTRADAY RAPIDS provider
 - Update tests for Fitbit steps intraday features
 - Add tests for phone battery features
 - Add a data cleaning module to replace NAs with 0 in selected event-based features, discard unreliable rows and columns, discard columns with zero variance, and discard highly correlated columns
+
 ## v1.6.0
+
 - Refactor PHONE_CALLS RAPIDS provider to compute features based on call episodes or events
 - Refactor PHONE_LOCATIONS DORYAB provider to compute features based on location episodes
 - Temporary revert PHONE_LOCATIONS BARNETT provider to use R script
 - Update the default IGNORE_EPISODES_LONGER_THAN to be 6 hours for screen RAPIDS provider
 - Fix the bug of step intraday features when INCLUDE_ZERO_STEP_ROWS is False
+
 ## v1.5.0
+
 - Update Barnett location features with faster Python implementation
 - Fix rounding bug in data yield features
 - Add tests for data yield, Fitbit and accelerometer features
 - Small fixes of documentation
+
 ## v1.4.1
+
 - Update home page
 - Add PHONE_MESSAGES tests
+
 ## v1.4.0
+
 - Add new Application Foreground episode features and tests
 - Update VSCode setup instructions for our Docker container
 - Add tests for phone calls features
@@ -52,7 +73,9 @@
 - Fix Fitbit bug that parsed date-times with the current time zone in rare cases
 - Update the visualizations to be more precise and robust with different time segments.
 - Fix regression crash of the example analysis workflow
+
 ## v1.3.0
+
 - Refactor PHONE_LOCATIONS DORYAB provider. Fix bugs and faster execution up to 30x
 - New PHONE_KEYBOARD features
 - Add a new strategy to infer home location that can handle multiple homes for the same participant
@@ -63,30 +86,40 @@
 - Remove location rows with the same timestamp based on their accuracy
 - Fix PHONE_CONVERSATION bug that produced inaccurate ratio features when time segments were not daily.
 - Other minor bug fixes
+
 ## v1.2.0
+
 - Sleep summary and intraday features are more consistent.
 - Add wake and bedtime features for sleep summary data.
 - Fix bugs with sleep PRICE features.
 - Update home page
 - Add contributing guide
+
 ## v1.1.1
+
 - Fix length of periodic segments on days with DLS
 - Fix crash when scraping data for an app that does not exist
 - Add tests for phone screen data
+
 ## v1.1.0
+
 - Add Fitbit calories intraday features
+
 ## v1.0.1
+
 - Fix crash in `chunk_episodes` of `utils.py` for multi time zone data
 - Fix crash in BT Doryab provider when the number of clusters is 2
 - Fix Fitbit multi time zone inference from phone data (simplify)
 - Fix missing columns when the input for phone data yield is empty
 - Fix wrong date time labels for event segments for multi time zone data (all labels are computed based on a single tz)
-- Fix periodic segment crash when there are no segments to assign (only affects wday, mday, qday, or yday) 
+- Fix periodic segment crash when there are no segments to assign (only affects wday, mday, qday, or yday)
 - Fix crash in Analysis Workflow with new suffix in segments' labels
+
 ## v1.0.0
+
 - Add a new [Overview](../setup/overview/) page.
 - You can [extend](../datastreams/add-new-data-streams/) RAPIDS with your own [data streams](../datastreams/data-streams-introduction/). Data streams are data collected with other sensing apps besides AWARE (like Beiwe, mindLAMP), and stored in other data containers (databases, files) besides MySQL.
-- Support to analyze Empatica wearable data (thanks to Joe Kim and  Brinnae Bent from the [DBDP](https://dbdp.org/))
+- Support to analyze Empatica wearable data (thanks to Joe Kim and Brinnae Bent from the [DBDP](https://dbdp.org/))
 - Support to analyze AWARE data stored in [CSV files](../datastreams/aware-csv/) and [InfluxDB](../datastreams/aware-influxdb/) databases
 - Support to analyze data collected over [multiple time zones](../setup/configuration/#multiple-timezones)
 - Support for [sleep intraday features](../features/fitbit-sleep-intraday/) from the core team and also from the community (thanks to Stephen Price)
@@ -98,22 +131,30 @@
 - Add new `time at home` Doryab location feature
 - Add and home coordinates to the location data file so location providers can build features based on it.
 - If you are migrating from RAPIDS 0.4.3 or older, check this [guide](../migrating-from-old-versions/#migrating-from-rapids-04x-or-older)
+
 ## v0.4.3
+
 - Fix bug when any of the rows from any sensor do not belong a time segment
+
 ## v0.4.2
+
 - Update battery testing
 - Fix location processing bug when certain columns don't exist
-- Fix HR intraday bug when minutesonZONE features were 0 
+- Fix HR intraday bug when minutesonZONE features were 0
 - Update FAQs
 - Fix HR summary bug when restinghr=0 (ignore those rows)
 - Fix ROG, location entropy and normalized entropy in Doryab location provider
 - Remove sampling frequency dependance in Doryab location provider
 - Update documentation of Doryab location provider
 - Add new `FITBIT_DATA_YIELD` `RAPIDS` provider
 - Deprecate Doryab circadian movement feature until it is fixed
+
 ## v0.4.1
+
 - Fix bug when no error message was displayed for an empty `[PHONE_DATA_YIELD][SENSORS]` when resampling location data
+
 ## v0.4.0
+
 - Add four new phone sensors that can be used for PHONE_DATA_YIELD
 - Add code so new feature providers can be added for the new four sensors
 - Add new clustering algorithm (OPTICS) for Doryab features
@@ -125,7 +166,9 @@
 - Fix bug when parsing Fitbit steps data
 - Fix bugs when merging features from empty time segments
 - Fix minor issues in the documentation
+
 ## v0.3.2
+
 - Update docker and linux instructions to use RSPM binary repo for for faster installation
 - Update CI to create a release on a tagged push that passes the tests
 - Clarify in DB credential configuration that we only support MySQL
@@ -135,38 +178,56 @@
 - Fixed Doryab location features context of clustering.
 - Fixed the wrong shifting while calculating distance in Doryab location features.
 - Refactored the haversine function
+
 ## v0.3.1
+
 - Update installation docs for RAPIDS' docker container
 - Fix example analysis use of accelerometer data in a plot
 - Update FAQ
 - Update minimal example documentation
 - Minor doc updates
+
 ## v0.3.0
+
 - Update R and Python virtual environments
 - Add GH actions CI support for tests and docker
 - Add release and test badges to README
+
 ## v0.2.6
+
 - Fix old versions banner on nested pages
+
 ## v0.2.5
+
 - Fix docs deploy typo
+
 ## v0.2.4
+
 - Fix broken links in landing page and docs deploy
+
 ## v0.2.3
+
 - Fix participant IDS in the example analysis workflow
+
 ## v0.2.2
+
 - Fix readme link to docs
+
 ## v0.2.1
+
 - FIx link to the most recent version in the old version banner
 
 ## v0.2.0
+
 - Add new `PHONE_BLUETOOTH` `DORYAB` provider
 - Deprecate `PHONE_BLUETOOTH` `RAPIDS` provider
 - Fix bug in `filter_data_by_segment` for Python when dataset was empty
 - Minor doc updates
 - New FAQ item
 
 ## v0.1.0
-- New and more consistent docs (this website). The [previous docs](https://rapidspitt.readthedocs.io/en/latest/) are marked as beta 
+
+- New and more consistent docs (this website). The [previous docs](https://rapidspitt.readthedocs.io/en/latest/) are marked as beta
 - Consolidate [configuration](../setup/configuration) instructions
 - Flexible [time segments](../setup/configuration#time-segments)
 - Simplify Fitbit behavioral feature extraction and [documentation](../features/fitbit-heartrate-summary)