Add src and some profiles

.github/workflows/CodeCov.yml

@@ -0,0 +1,44 @@
+name: CodeCov
+
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  codecov:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/[email protected]
+
+    - name: Set up Julia
+      uses: julia-actions/setup-julia@latest
+      with:
+        version: 1.7.0
+
+    - name: Test with coverage
+      env:
+        JULIA_PROJECT: "@."
+      run: |
+        julia --project=@. -e 'using Pkg; Pkg.instantiate()'
+        julia --project=@. -e 'using Pkg; Pkg.test(coverage=true)'
+
+    - name: Generate coverage file
+      env:
+        JULIA_PROJECT: "@."
+      run: julia --project=@. -e 'using Pkg; Pkg.add("Coverage");
+                                  using Coverage;
+                                  LCOV.writefile("coverage-lcov.info", Codecov.process_folder())'
+      if: success()
+
+    - name: Submit coverage
+      uses: codecov/[email protected]
+      with:
+        token: ${{secrets.CODECOV_TOKEN}}
+      if: success()
+

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: '00 00 * * *'
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}  # optional
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/DocCleanUp.yml

@@ -0,0 +1,28 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+
+      - name: Delete preview and history
+        run: |
+            git config user.name "Documenter.jl"
+            git config user.email "[email protected]"
+            git rm -rf "previews/PR$PRNUM"
+            git commit -m "delete preview"
+            git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+        env:
+            PRNUM: ${{ github.event.number }}
+
+      - name: Push changes
+        run: |
+            git push --force origin gh-pages-new:gh-pages

.github/workflows/TagBot.yml

@@ -0,0 +1,67 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          changelog: |
+            ## {{ package }} {{ version }}
+            {% if previous_release %}
+            [Diff since {{ previous_release }}]({{ compare_url }})
+            {% endif %}
+            {% if custom %}
+            {{ custom }}
+            {% endif %}
+            ### 📢 API Changes:
+            {% if issues %}
+            {% for issue in issues if 'API' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'API' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}
+            ### 🚀 Features
+            {% if issues %}
+            {% for issue in issues if 'enhancement' in issue.labels or 'feature' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'enhancement' in pull.labels or 'feature' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}
+            ### 📑 Documentation
+            {% if issues %}
+            {% for issue in issues if 'documentation' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'documentation' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}
+            ### 🐛 Fixes
+            {% if issues %}
+            {% for issue in issues if 'bug' in issue.labels or 'bugfix' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'bug' in pull.labels or 'bugfix' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: ci
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  test:
+    name: ci ${{ matrix.version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.7.0'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      # - uses: actions/cache@v1
+      #   env:
+      #     cache-name: cache-artifacts
+      #   with:
+      #     path: ~/.julia/artifacts
+      #     key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+      #     restore-keys: |
+      #       ${{ runner.os }}-test-${{ env.cache-name }}-
+      #       ${{ runner.os }}-test-
+      #       ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/docs.yml

@@ -0,0 +1,26 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  docbuild:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1.7.0
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.gitignore

@@ -16,6 +16,11 @@ deps/src/
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+# Auto-generated file
+docs/src/generated_profile_library.md
+
+# Data files
+*.png
 
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be

Project.toml

@@ -0,0 +1,11 @@
+name = "AtmosphericProfilesLibrary"
+uuid = "86bc3604-9858-485a-bdbe-831ec50de11d"
+authors = ["Charles Kawczynski <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
+
+[compat]
+Dierckx = "0.5"
+julia = "1"

README.md

@@ -1,2 +1,25 @@
 # AtmosphericProfilesLibrary.jl
+
 A library of atmospheric profiles
+
+|||
+|---------------------:|:----------------------------------------------|
+| **Docs Build**       | [![docs build][docs-bld-img]][docs-bld-url]   |
+| **Documentation**    | [![dev][docs-dev-img]][docs-dev-url]          |
+| **GHA CI**           | [![gha ci][gha-ci-img]][gha-ci-url]           |
+| **Bors enabled**     | [![bors][bors-img]][bors-url]                 |
+
+[docs-bld-img]: https://github.com/CliMA/AtmosphericProfilesLibrary.jl/actions/workflows/docs.yml/badge.svg
+[docs-bld-url]: https://github.com/CliMA/AtmosphericProfilesLibrary.jl/actions/workflows/docs.yml
+
+[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
+[docs-dev-url]: https://CliMA.github.io/AtmosphericProfilesLibrary.jl/dev/
+
+[gha-ci-img]: https://github.com/CliMA/AtmosphericProfilesLibrary.jl/actions/workflows/ci.yml/badge.svg
+[gha-ci-url]: https://github.com/CliMA/AtmosphericProfilesLibrary.jl/actions/workflows/ci.yml
+
+[bors-img]: https://bors.tech/images/badge_small.svg
+[bors-url]: https://app.bors.tech/repositories/41911
+
+See our [docs](https://CliMA.github.io/AtmosphericProfilesLibrary.jl/dev/) for usage and how to contribute.
+

docs/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+AtmosphericProfilesLibrary = "86bc3604-9858-485a-bdbe-831ec50de11d"
+Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+
+[compat]
+Dierckx = "0.5"

docs/bibliography.bib

@@ -0,0 +1,26 @@
+# The citation keys have been formatted as:
+#    Last author name (titlecase), followed by
+#    (no characters in-between) the year.
+
+@article{Grabowski2006,
+  title = {Daytime convective development over land: A model intercomparison based on LBA observations},
+  author = {Grabowski, WW and Bechtold, P and Cheng, A and Forbes, R and Halliwell, C and Khairoutdinov, M and Lang, S and Nasuno, T and Petch, J and Tao, W-K and others},
+  journal = {Quarterly Journal of the Royal Meteorological Society: A journal of the atmospheric sciences, applied meteorology and physical oceanography},
+  volume = {132},
+  number = {615},
+  pages = {317--344},
+  year = {2006},
+  publisher = {Wiley Online Library}
+}
+
+@article{Soares2004,
+  title = {An eddy-diffusivity/mass-flux parametrization for dry and shallow cumulus convection},
+  author = {Soares, PMM and Miranda, PMA and Siebesma, AP and Teixeira, J},
+  journal = {Quarterly Journal of the Royal Meteorological Society: A journal of the atmospheric sciences, applied meteorology and physical oceanography},
+  volume = {130},
+  number = {604},
+  pages = {3365--3383},
+  year = {2004},
+  publisher = {Wiley Online Library},
+  doi = {https://doi.org/10.1256/qj.03.223}
+}

docs/generate_profile_library.jl

@@ -0,0 +1,62 @@
+
+# Generate figures:
+include(joinpath(@__DIR__, "src", "plot_profiles.jl"))
+
+prof_lib = joinpath(@__DIR__, "src", "generated_profile_library.md")
+open(prof_lib, "w") do io
+
+    println(io, "```@meta")
+    println(io, "# ****************************************************")
+    println(io, "# ****************************************************")
+    println(io, "#     THIS FILE IS AUTO-GENERATED, PLEASE DO NOT EDIT.")
+    println(io, "# ****************************************************")
+    println(io, "# ****************************************************")
+    println(io, "```")
+
+    println(io, "# Profile library")
+
+    println(io, "")
+    println(io, "```@meta")
+    println(io, "CurrentModule = AtmosphericProfilesLibrary")
+    println(io, "```")
+
+    println(io, "")
+    println(io, "```@example")
+    println(io, "include(joinpath(@__DIR__, \"plot_profiles.jl\"))")
+    println(io, "```")
+    println(io, "")
+
+    println(io, "## z-profiles")
+    for profile in z_profiles
+        fname = nameof(profile.func)
+        println(io, "```@docs")
+        println(io, "$fname")
+        println(io, "```")
+        println(io, "![](z_$fname.png)")
+        println(io, "")
+    end
+
+    if !isempty(t_profiles)
+        println(io, "## t-profiles")
+        for profile in t_profiles
+            fname = nameof(profile.func)
+            println(io, "```@docs")
+            println(io, "$fname")
+            println(io, "```")
+            println(io, "![](t_$fname.png)")
+            println(io, "")
+        end
+    end
+
+    println(io, "## tz-profiles")
+    for profile in tz_profiles
+        fname = nameof(profile.func)
+        println(io, "```@docs")
+        println(io, "$fname")
+        println(io, "```")
+        println(io, "![](tz_$fname.png)")
+        println(io, "")
+    end
+end
+
+@assert isfile(prof_lib)