Merge branch 'master' into documentation-edits

tardis-sn · May 21, 2020 · 8846944 · 8846944
2 parents 6429237 + cddd9a6
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diff --git a/.gitignore b/.gitignore
@@ -17,12 +17,17 @@ __pycache__
 */cython_version.py
 htmlcov
 .coverage
+.ipynb_checkpoints/
 
 
 # IDE Specific files
 ### Pycharm IDE - Jetbrains
 .idea/*
 
+# VSCode
+.vscode/
+*.code-workspace
+
 ### PyDev IDE - Eclipse
 .metadata
 tmp/
@@ -40,11 +45,13 @@ local.properties
 
 # Sphinx
 _build
+docs/api
 
 
 # Packages/installer info
 *.egg
 *.egg-info
+.eggs/
 dist
 build
 eggs
@@ -64,3 +71,6 @@ distribute-*.tar.gz
 
 # Mac OSX
 .DS_Store
+
+# Jupyter checkpoints
+.ipynb_checkpoints
diff --git a/.mailmap b/.mailmap
@@ -116,3 +116,10 @@ Andreas Flörs <afloers@mpa-garching.mpg.de> Andreas Flörs <33418619+afloers@us
 Alice Harpole <aliceharpole@gmail.com>
 Alice Harpole <aliceharpole@gmail.com> Alice Harpole <harpolea@users.noreply.github.com>
 
+Sampark Sharma <samparksharma2000@gmail.com>
+
+Jordi Eguren <jordi.eguren.brown@gmail.com>
+Jordi Eguren <jordi.eguren.brown@gmail.com> Jordi Eguren <45364266+jordi5@users.noreply.github.com>
+
+Atul Kumar <kr.atul.atk@gmail.com>
+
diff --git a/.zenodo.json b/.zenodo.json
@@ -90,10 +90,10 @@
       "name": "Barna, Barnab\u00e1s"
     },
     {
-      "name": "Barbosa, Talytha"
+      "name": "Gautam, Gaurav"
     },
     {
-      "name": "Gautam, Gaurav"
+      "name": "Barbosa, Talytha"
     },
     {
       "name": "Patel, Maryam"
@@ -122,36 +122,57 @@
     {
       "name": "Reichenbach, John"
     },
+    {
+      "name": "Singhal, Jaladh"
+    },
     {
       "name": "Jain, Rinkle"
     },
     {
       "name": "Singh, Sourav"
     },
     {
-      "name": "Talegaonkar, Chinmay"
+      "name": "Pipelines, Azure"
     },
     {
       "name": "Kowalski, Nathan"
     },
     {
       "name": "Sofiatti, Caroline"
     },
+    {
+      "name": "Talegaonkar, Chinmay"
+    },
     {
       "name": "Selsing, Jonatan"
     },
+    {
+      "name": "Savel, Arjun"
+    },
+    {
+      "name": "Nayak, Ashwin"
+    },
     {
       "name": "Wahi, Ujjwal"
     },
     {
-      "name": "Sarafina, Nance"
+      "name": "Kumar, Atul"
     },
     {
-      "name": "Gillanders, James"
+      "name": "Mishra, Sashank"
     },
     {
       "name": "Dasgupta, Debajyoti"
     },
+    {
+      "name": "Gillanders, James"
+    },
+    {
+      "name": "Sharma, Sampark"
+    },
+    {
+      "name": "Eguren, Jordi"
+    },
     {
       "name": "Gupta, Suyash"
     },
@@ -162,10 +183,13 @@
       "name": "Magee, Mark"
     },
     {
-      "name": "Patel, Pratik"
+      "name": "Sarafina, Nance"
     },
     {
       "name": "Patra, Nilesh"
+    },
+    {
+      "name": "Patel, Pratik"
     }
   ]
 }
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,60 @@
+# TARDIS Community Code of Conduct
+
+The community of participants in open source Astronomy 
+projects is made up of members from around the globe 
+with a diverse set of skills, personalities, and 
+experiences. It is through these differences that our 
+community experiences success and continued growth. 
+We expect everyone in our community to follow these 
+guidelines when interacting with others both inside 
+and outside of our community. Our goal is to keep ours 
+a positive, inclusive, successful, and growing community.
+
+As members of the community,
+
+* We pledge to treat all people with respect and provide 
+a harassment- and bullying-free environment, regardless 
+of sex, sexual orientation and/or gender identity, 
+disability, physical appearance, body size, race, 
+nationality, ethnicity, and religion. In particular, 
+sexual language and imagery, sexist, racist, or 
+otherwise exclusionary jokes are not appropriate.
+* We pledge to respect the work of others by recognizing 
+acknowledgment/citation requests of original authors. As 
+authors, we pledge to be explicit about how we want our 
+own work to be cited or acknowledged.
+* We pledge to welcome those interested in joining the 
+community, and realize that including people with a variety 
+of opinions and backgrounds will only serve to enrich our 
+community. In particular, discussions relating to pros/cons 
+of various technologies, programming languages, and so on are 
+welcome, but these should be done with respect, taking proactive 
+measure to ensure that all participants are heard and feel 
+confident that they can freely express their opinions.
+* We pledge to welcome questions and answer them respectfully, 
+paying particular attention to those new to the community. We 
+pledge to provide respectful criticisms and feedback in forums, 
+especially in discussion threads resulting from code contributions.
+* We pledge to be conscientious of the perceptions of the wider 
+community and to respond to criticism respectfully. We will strive 
+to model behaviors that encourage productive debate and disagreement, 
+both within our community and where we are criticized. We will treat 
+those outside our community with the same respect as people within 
+our community.
+* We pledge to help the entire community follow the code of conduct, 
+and to not remain silent when we see violations of the code of conduct. 
+We will take action when members of our community violate this code 
+such as contacting lead developers of the TARDIS team.
+
+
+This code of conduct applies to all community situations online and 
+offline, including mailing lists, forums, social media, conferences, 
+meetings, associated social events, and one-to-one interactions.
+
+Any related activity or project organized by members of the TARDIS 
+community, including affiliated packages, are welcome to have their 
+own codes of conduct, but agree to also abide by the present code of 
+conduct.
+
+This code of conduct has been adapted from the Astropy Code of Conduct,
+which in turn uses parts of the PSF code of conduct.
diff --git a/README.rst b/README.rst
@@ -84,7 +84,7 @@ The following bibtex entries are needed for the references.
     }
 
 
-    @misc{kerzendorf_wolfgang_2019_2590539,
+    @software{kerzendorf_wolfgang_2019_2590539,
       author       = {Kerzendorf, Wolfgang and
                       Nöbauer, Ulrich and
                       Sim, Stuart and

diff --git a/azure-pipelines/compare-refdata.yml b/azure-pipelines/compare-refdata.yml
@@ -3,6 +3,9 @@
 # Add steps that build, run tests, deploy, and more:
 # https://aka.ms/yaml
 
+trigger: none
+pr: none
+
 variables:
   system.debug: "true"
   ref.data.home: "$(Agent.BuildDirectory)/tardis-refdata"

diff --git a/azure-pipelines/release-version.yml b/azure-pipelines/release-version.yml
@@ -15,92 +15,14 @@ schedules:
 
 variables:
   system.debug: "true"
-  tardis.zenodo.home: "$(Agent.BuildDirectory)/tardis_zenodo"
   tardis.build.dir: $(Build.Repository.LocalPath)
 
 pool:
   vmImage: "ubuntu-latest"
 
 jobs:
-  - job: zenodo_json
-    displayName: Create Zenodo JSON file
-    steps:
-      - task: DownloadSecureFile@1
-        name: zenodoSecretKey
-        displayName: "Download Zenodo secret key"
-        inputs:
-          secureFile: "key_secret.json"
-
-      - task: DownloadSecureFile@1
-        name: authorOrder
-        displayName: "Download author order file"
-        inputs:
-          secureFile: "author_order.txt"
-
-      - task: DownloadSecureFile@1
-        name: nonCommitContributors
-        displayName: "Download non commit contributors file"
-        inputs:
-          secureFile: "non_commit_contributors.txt"
-
-      - bash: |
-          echo "##vso[task.prependpath]$CONDA/bin"
-          sudo chown -R $USER $CONDA
-        displayName: "Add CONDA to path"
-
-      - bash: |
-          conda create -n zenodo python=3.6 --yes
-          source activate zenodo
-          conda install jupyter nbconvert numpy pandas orcid -c conda-forge --yes
-        displayName: "Create Zenodo env"
-
-      # Actually this is a workaround. We need to grab this from `tardis_zenodo` private repo.
-      - bash: |
-          cd ..; mkdir tardis_zenodo
-          cd $(tardis.zenodo.home)
-          wget https://gist.githubusercontent.com/epassaro/12364cd3b33e4b2923ff1861d80ef6d8/raw/d71ca46ca1816f6f46c768314c2da59ed017861e/gather_data.ipynb
-        displayName: "Downloading notebook (workaround)"
-
-      - bash: |
-          cp $(zenodoSecretKey.secureFilePath) $(tardis.zenodo.home)
-          cp $(authorOrder.secureFilePath) $(tardis.zenodo.home)
-          cp $(nonCommitContributors.secureFilePath) $(tardis.zenodo.home)
-        displayName: "Recovering secrets"
-
-      - bash: |
-          source activate zenodo
-          cd $(tardis.zenodo.home)
-          jupyter nbconvert gather_data.ipynb --to html --allow-errors --execute --ExecutePreprocessor.timeout=6000
-        displayName: "Running notebook (allow errors)"
-
-      - bash: |
-          source activate zenodo
-          cd $(tardis.zenodo.home)
-          jupyter nbconvert gather_data.ipynb --to html --execute --ExecutePreprocessor.timeout=6000
-        displayName: "Running notebook (not allow errors)"
-
-      # This step should fail if there are changes in .zenodo.json
-      - bash: |
-          diff $(tardis.zenodo.home)/.zenodo.json .zenodo.json
-        displayName: "Look for changes in JSON"
-
-      - task: PublishPipelineArtifact@1
-        inputs:
-          targetPath: "$(tardis.zenodo.home)/.zenodo.json"
-          artifact: "zenodo_json"
-          publishLocation: "pipeline"
-        condition: succeededOrFailed()
-
-      - task: PublishPipelineArtifact@1
-        inputs:
-          targetPath: "$(tardis.zenodo.home)/gather_data.html"
-          artifact: "report"
-          publishLocation: "pipeline"
-        condition: succeededOrFailed()
-
   - job: gh_release
     displayName: Upload GitHub release
-    dependsOn: zenodo_json
     steps:
       - bash: |
           echo "##vso[task.prependpath]$CONDA/bin"

diff --git a/azure-pipelines/simple_test_framework.yml b/azure-pipelines/simple_test_framework.yml
@@ -28,7 +28,7 @@ jobs:
         vm_Image: 'Ubuntu-16.04'
         conda: '/usr/share/miniconda'
       mac:
-        vm_Image: 'macOS-10.13'
+        vm_Image: 'macOS-10.14'
         miniconda.url: 'http://repo.continuum.io/miniconda/Miniconda2-latest-mac-x86_64.sh'
     maxParallel: 4
 
@@ -63,16 +63,6 @@ jobs:
         pytest tardis --tardis-refdata=$(ref.data.home) --cov=tardis --cov-report=xml --cov-report=html
         export QT_API=pyqt
     displayName: 'TARDIS test'
-
-
-#  - task: PublishTestResults@2
-#    condition: succeededOrFailed()
-#    inputs:
-#      testResultsFiles: '**/test-*.xml'
-#      testRunTitle: 'Test results for TARDIS on $(vm_Image)'
-
-#  - task: PublishCodeCoverageResults@1
-#    inputs:
-#      codeCoverageTool: Cobertura
-#      summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
-#      reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
+  - script: |
+      bash <(curl -s https://codecov.io/bash)
+    displayName: 'Upload to codecov.io'