Merge pull request #41 from dapperstats/feature

workflows

.github/workflows/docker-publish.yml

@@ -0,0 +1,62 @@
+# build and publish the docker image when the version is tagged under semantic versioning
+# the cron job release tags are formatted using date-time stamp, not semantic version, allowing for differentiation
+# based on https://github.com/docker/build-push-action
+
+name: docker_image_publish
+
+on:
+  push:
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ main ]
+
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: ${{ github.repository }}
+  DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+
+
+jobs:
+  build_docker_image:
+    name: build docker image
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log into ${{ env.REGISTRY }} except on PR
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ env.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: crazy-max/ghaction-docker-meta@v1
+        with:
+          images: dapperstats/salvage
+          tag-custom: latest
+          tag-semver: |
+            {{raw}}   
+
+      - name: Build and push Docker image except on PR
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }} 
+#           tags: dapperstats/salvage:latest
+          labels: ${{ steps.meta.outputs.labels }}
+          file: docker/Dockerfile

CODE_OF_CONDUCT.md

@@ -40,5 +40,4 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 1.4, 
-available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

CONTRIBUTING.md

@@ -73,8 +73,4 @@ For more info, see the [GitHub repo](https://github.com/hadley/devtools) for the
 
 ## Attribution 
 
-This document is based on the [CONTRIBUTING 
-file](https://github.com/weecology/portalr/blob/master/CONTRIBUTING.md)
-associated with the Beta release of the 
-[**portalr**](https://github.com/weecology/portalr/) package
-and is used under the MIT License.
+This document is based on the [CONTRIBUTING file](https://github.com/weecology/portalr/blob/main/CONTRIBUTING.md) associated with the Beta release of the [**portalr**](https://github.com/weecology/portalr/) package and is used under the MIT License.

NEWS.md

@@ -2,6 +2,16 @@
 
 Version numbers follow [Semantic Versioning](https://semver.org/).
 
+# [v0.9.0](https://github.com/dapperstats/salvage/releases/tag/v0.9.0)
+*2022-12-02*
+
+## Shifting build workflow from travis to Github Actions
+* cron workflow implementing the image-based pipeline
+* tag workflow building and publishing image updates
+* both workflows proceed but do not finish on PRs
+
+## Move dockerfile into a folder
+* Create a docker folder for holding dockerfile and readme
 
 # [v0.8.0](https://github.com/dapperstats/salvage/releases/tag/v0.8.0) 
 *2020-01-29*
@@ -70,7 +80,7 @@ Version numbers follow [Semantic Versioning](https://semver.org/).
   * `.travis.yml` leverages the non-interactive image to build only the `.csv` files (no `R` session is started)
   * `update_github_data.bash` is what's run `after_success` for `cron` jobs only
     * Uses @dapperdeploy as the user bpt
-    * Updates the master branch with the `.csv`s and `.txt` date log
+    * Updates the main branch with the `.csv`s and `.txt` date log
     * Creates a tag based on the date, and deploys the tag as a release
 
 
@@ -87,7 +97,7 @@ Version numbers follow [Semantic Versioning](https://semver.org/).
 ## Updated `Docker` image
 * [v0.2.0](https://hub.docker.com/layers/dapperstats/salvage/0.2.0/images/sha256-224f226aa90eb94a6730c7e95f5f8013bc2c150258d090c0df6e97769a3ef044)
 
-## Inclusion of this here [`NEWS`](https://github.com/dapperstats/salvage/blob/master/NEWS.md)
+## Inclusion of this here [`NEWS`](https://github.com/dapperstats/salvage/blob/main/NEWS.md)
 
 # [v0.1.0](https://github.com/dapperstats/salvage/releases/tag/v0.1.0) 
 *2020-01-12*

README.md

@@ -17,7 +17,7 @@ One present focus is reliably generating data products that are more broadly acc
 Each day, the [`/data` directory](https://github.com/dapperstats/salvage/blob/main/data) is populated with `.csv`s from an up-to-date "current" (1993 - Present) salvage database file (`Salvage_data_FTP.accdb`).
 The `.csv` files are then used to update the [data presentation website (salvage.fish)](https://salvage.fish).
 
-Updates are executed via [`cron` jobs](https://docs.travis-ci.com/user/cron-jobs/) on [`travis-ci`](https://travis-ci.org/dapperstats/salvage) using the `accessor` [`Docker`](https://www.docker.com) [software container](https://www.docker.com/resources/what-container).
+Updates are executed via [`cron` jobs](https://en.wikipedia.org/wiki/Cron) on [`Github Actions`](https://github.com/dapperstats/salvage/actions) using the `accessor` [`Docker`](https://www.docker.com) [software container](https://www.docker.com/resources/what-container).
 Code for the construction of the [`accessor` image](https://hub.docker.com/r/dapperstats/accessor) is available in a [separate repo](https://www.github.com/dapperstats/accessor).
 
 Read more details on the [methods](https://github.com/dapperstats/salvage/blob/main/documents/methods.md), including how to run your own data [conversions](https://github.com/dapperstats/salvage/blob/main/documents/conversion.md).

docker/README.md

@@ -0,0 +1,13 @@
+#  [salvage.fish](https://www.salvage.fish)
+
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/dapperstats/salvage/main/LICENSE)
+[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3628045.svg)](https://doi.org/10.5281/zenodo.3628045)
+
+Tools for smooth interactions with the [California Delta](https://en.wikipedia.org/wiki/Sacramento%E2%80%93San_Joaquin_River_Delta) [fish salvage monitoring database](https://wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring).
+
+This image includes the R-based script and functions for reading in the converted data files, analyzing, and vizualizing the results, including production of the website output. 
+
+The image is built using the [`Docker` GitHub Action](https://github.com/dapperstats/salvage/actions/workflows/docker-publish.yml) for any pull request in the `salvage` repository but is only pushed to [Docker Hub](https://hub.docker.com/repository/docker/dapperstats/salvage) upon creation of a release tagged under semantic versioning. 
+
+Two copies of the image are pushed to Docker Hub: one tagged with the release version and one tagged as "latest"..

documents/methods.md

@@ -3,19 +3,19 @@
 ## Data Access
 
 
-<br>
+### Retrieve the [Salvage Database]((https://filelib.wildlife.ca.gov/Public/salvage/)
 
-### Retrieve the Salvage Database
+Source data are freely available from the [California Department of Fish and Wildlife](https://wildlife.ca.gov) [Fish Salvage Monitoring Program](https://wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring) on a [public data server](https://filelib.wildlife.ca.gov/Public/salvage/).
 
-The bulk of the data access protocol involves converting the `.accdb` salvagae database file on the remote [ftp](ftp://ftp.dfg.ca.gov/salvage/) to a local set of `.csv` files named by the tables in the database. 
+The bulk of the data access protocol involves converting the `.accdb` salvage database file on the remote [server](https://wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring) to a local set of `.csv` files named by the tables in the database. 
 We accomplish this in two lines of code by pulling and then running a stable [`Docker`](https://www.docker.com) [software container](https://www.docker.com/resources/what-container) that contains a set of `bash` scripts designed specifically for this task.
 The specific image used for data access is called [`accessor`](https://hub.docker.com/r/dapperstats/accessor), is freely available on [Docker Hub](https://hub.docker.com/), and has default setting configured for the salvage database.
 Code for the construction of the `accessor` image is available in its [repository](https://www.github.com/dapperstats/accessor).
 
-For accessability and reproducibility, we provide an [up-to-date version of the salvage data](https://github.com/dapperstats/salvage/blob/master/data) as `.csv`s from the "current" (1993 - Present) salvage database file (`Salvage_data_FTP.accdb`).
+For accessability and reproducibility, we provide an [up-to-date version of the salvage data](https://github.com/dapperstats/salvage/blob/main/data) as `.csv`s from the "current" (1993 - Present) salvage database file (`Salvage_data_FTP.accdb`).
 The data can be downloaded via various methods from the repository, including from the website.
 
-Updates to the data are executed via [`cron` jobs](https://docs.travis-ci.com/user/cron-jobs/) on [`travis-ci`](https://travis-ci.org/dapperstats/salvage) and pushed to GitHub as [tagged Releases](https://github.com/dapperstats/salvage/releases).
+Updates are executed via [`cron` jobs](https://en.wikipedia.org/wiki/Cron) on [`Github Actions`](https://github.com/dapperstats/salvage/actions)  and pushed to GitHub as [tagged Releases](https://github.com/dapperstats/salvage/releases).
 
 <br> 
 
@@ -43,9 +43,9 @@ sudo docker cp salvage:/data .
 
 ### Bring the Data into R 
 
-An additional conversion makes the data available in [`R`](https://www.r-project.org/) as a `list` of `data.frames` that is directly analagous to the `.accdb` database of tables.
+An additional conversion makes the data available in [`R`](https://www.r-project.org/) as a `list` of `data.frames` that is directly analogous to the `.accdb` database of tables.
 
-The reading into R is conducted via functions included in the `r_functions.R` script in the [`accessor` image](https://hub.docker.com/r/dapperstats/accessor) and available in the [public code repository](https://github.com/dapperstats/accessor/tree/master/scripts).
+The reading into R is conducted via functions included in the `r_functions.R` script in the [`accessor` image](https://hub.docker.com/r/dapperstats/accessor) and available in the [public code repository](https://github.com/dapperstats/accessor/tree/main/scripts).
 
 <br>
 
@@ -102,11 +102,11 @@ The resulting `database` object is a named `list` of the database's tables, read
 Data preparation code is *in development*!
 
 Having brought the data into R as-is, we can now prepare them for summaries and analyses.
-We use the functions included in the [`salvage_functions.R` R script](https://github.com/dapperstats/salvage/blob/master/scripts/salvage_functions.R), which is included within the and [`salvage` docker image](https://hub.docker.com/r/dapperstats/salvage), which provides a stable runtime environment for the analyses and output generation (including website rendering).
+We use the functions included in the [`salvage_functions.R` R script](https://github.com/dapperstats/salvage/blob/main/scripts/salvage_functions.R), which is included within the and [`salvage` docker image](https://hub.docker.com/r/dapperstats/salvage), which provides a stable runtime environment for the analyses and output generation (including website rendering).
 
 <br>
 
 ## Continuous Deployment
 
-The data and output are updated daily via [`cron` jobs](https://docs.travis-ci.com/user/cron-jobs/) on [`travis-ci`](https://travis-ci.org/dapperstats/salvage) with a recipe (a.k.a. job lifecycle) described by the [`.travis.yml` file](https://github.com/dapperstats/salvage/blob/master/.travis.yml).
+Updates are executed via [`cron` jobs](https://en.wikipedia.org/wiki/Cron) on [`Github Actions`](https://github.com/dapperstats/salvage/actions) with a workflow described by the [`docker_cron.yaml` file](https://github.com/dapperstats/salvage/blob/main/.github/workflows/docker_cron.yaml).