Merge branch 'main' into validation_test1

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,140 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation
+in our Scenario Modeling Hub community a harassment-free experience
+for everyone, regardless of age, body size, visible or invisible
+disability, ethnicity, sex characteristics, gender identity and
+expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, political
+affiliation, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, 
+welcoming, diverse, inclusive, and healthy community.
+
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our 
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, 
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall 
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances 
+  of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others’ private information, such as a physical or email address, 
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a 
+  professional setting
+
+
+## Enforcement Responsibilities
+
+The code of conduct committee is responsible for clarifying and
+enforcing our standards of acceptable behavior and will take
+appropriate and fair corrective action in response to any behavior
+that they deem inappropriate, threatening, offensive, or harmful.
+
+The code of conduct committee has the right and responsibility to
+remove, edit, or reject comments, commits, code, wiki edits, issues,
+and other contributions that are not aligned to this Code of Conduct,
+and will communicate reasons for moderation decisions when
+appropriate.
+
+The SMH code of conduct committee consists of three members:
+
+- [Lucie Contamin](mailto:[email protected])
+- [Emily Howerton](mailto:[email protected])
+- [Bryan Lewis](mailto:[email protected])
+
+
+## Scope
+
+This Code of Conduct applies within all Scenario Modeling Hub public online 
+shared resources (e.g. GitHub, shared Slack channels).
+
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported to the code of conduct committee responsible for
+enforcement by email. All complaints will be reviewed and
+investigated promptly and fairly. 
+
+All members of the code of conduct committee are obligated to respect 
+the privacy and security of the reporter of any incident.
+
+
+## Enforcement Guidelines
+
+The code of conduct committee will follow these Community Impact 
+Guidelines in determining the consequences for any action they 
+deem in violation of this Code of Conduct:
+
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior 
+deemed unprofessional or unwelcome in the community.
+
+**Consequence**:  A private, written warning from the code of conduct 
+committee, providing clarity around the nature of the violation and an 
+explanation of why the behavior was inappropriate. A public apology may 
+be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of 
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No 
+interaction with the people involved, including unsolicited interaction 
+with those enforcing the Code of Conduct, for a specified period of time. 
+This includes avoiding interactions in community spaces as well as external 
+channels like social media. Violating these terms may lead to a temporary 
+or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including 
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public 
+communication with the community for a specified period of time. No public 
+or private interaction with the people involved, including unsolicited 
+interaction with those enforcing the Code of Conduct, is allowed during 
+this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community 
+standards, including sustained inappropriate behavior, harassment of an 
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within 
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the 
+[Contributor Covenant](https://www.contributor-covenant.org), 
+version 2.1, available at 
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by 
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at 
+<https://www.contributor-covenant.org/faq>. 
+Translations are available at <https://www.contributor-covenant.org/translations>.

.github/workflows/install_cache_dependencies.yml

@@ -32,7 +32,7 @@ jobs:
             R -e 'Sys.setenv("NOT_CRAN" = TRUE)
                   install.packages(c("arrow", "gh", "remotes"))
                   Sys.unsetenv("NOT_CRAN")
-                  remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/main.zip")
+                  remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/version.zip")
                   remotes::install_url("https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/archive/refs/heads/main.zip")'
-          env: 
+          env:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/validation.yml

@@ -1,8 +1,11 @@
-name: Validate Submission(s)
+name: Validate Submission
 on:
   pull_request_target:
+    types: [synchronize, opened, reopened]
     branches:
       - main
+    paths: 
+      - 'data-processed/**.parquet'
 
 jobs:
     validates-files:
@@ -15,34 +18,45 @@ jobs:
             fetch-depth: 1
 
         - name: Setup R
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: r-lib/actions/setup-r@v2
 
         - name: Install system dependencies
           run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
 
 
-        - name: Cache R packages 
+        - name: Cache R packages
           id: cache
-          if: runner.os != 'Windows' 
-          uses: actions/cache@v2 
-          with: 
-            path: ${{ env.R_LIBS_USER }} 
+          uses: actions/cache@v2
+          with:
+            path: ${{ env.R_LIBS_USER }}
             key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
 
         - name: Install dependencies
-          if: steps.cache.outputs.cache-hit != 'true'
+          if: ( steps.cache.outputs.cache-hit != 'true' )
           run: |
             R -e 'Sys.setenv("NOT_CRAN" = TRUE)
                   install.packages(c("arrow", "gh", "remotes"))
                   Sys.unsetenv("NOT_CRAN")
-                  remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/main.zip")
+                  remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/version.zip")
                   remotes::install_url("https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/archive/refs/heads/main.zip")'
-          env: 
+          env:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-        - name: Run Validation
+
+        - name: Run Validation - Open/reopen
+          if: ( github.event.action != 'synchronize' )
+          run: |
+            Rscript code/validation.R
+          env:
+            GH_PR_NUMBER: ${{ github.event.pull_request.number }}
+            GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+        - name: Run Validation - Synchronize
+          if: ( github.event.action == 'synchronize' )
           run: |
             Rscript code/validation.R
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
+