Update gas mixture example, add CI

.github/workflows/ci.yml

@@ -0,0 +1,149 @@
+name: xrayAttenuation CI
+on:
+  push:
+    paths:
+      - 'tests/**'
+      - 'src/**'
+      - 'docs/**'
+      - 'xrayAttenuation.nimble'
+      - '.github/workflows/ci.yml'
+    branches:
+      - 'master'
+  pull_request:
+    paths:
+      - 'tests/**'
+      - 'src/**'
+      - 'docs/**'
+      - 'xrayAttenuation.nimble'
+      - '.github/workflows/ci.yml'
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        nim:
+          #- '1.6.x'
+          - '2.0.x'
+          - 'devel'
+        os:
+          - ubuntu-latest
+          - windows-latest
+          - macOS-latest
+    name: '${{ matrix.nim }} (${{ matrix.os }})'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          path: xrayAttenuation
+
+      - name: Setup nim
+        uses: jiro4989/setup-nim-action@v1
+        with:
+          nim-version: ${{ matrix.nim }}
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies (Ubuntu)
+        if: ${{matrix.os == 'ubuntu-latest'}}
+        run: |
+          sudo apt-get update
+          sudo apt-get install musl musl-dev musl-tools
+
+      - name: Setup nimble & deps
+        shell: bash
+        run: |
+          cd xrayAttenuation
+          nimble refresh -y
+          nimble install -y
+          nimble ciDeps -y
+
+      - name: Run tests
+        shell: bash
+        run: |
+          cd xrayAttenuation
+          nimble -y test
+
+      - name: Build docs
+        if: ${{ matrix.docs == 'true' && matrix.os == 'ubuntu-latest' }}
+        shell: bash
+        run: |
+          cd xrayAttenuation
+          branch=${{ github.ref }}
+          branch=${branch##*/}
+          nimble doc --project --outdir:docs \
+            '--git.url:https://github.com/${{ github.repository }}' \
+            '--git.commit:${{ github.sha }}' \
+            "--git.devel:$branch" \
+            xrayAttenuation.nim
+          # Ignore failures for older Nim
+          cp docs/{the,}index.html || true
+
+      - name: Publish docs
+        if: >
+          github.event_name == 'push' && github.ref == 'refs/heads/master' &&
+          matrix.os == 'ubuntu-latest' && matrix.nim == 'devel'
+        uses: crazy-max/ghaction-github-pages@v1
+        with:
+          build_dir: xrayAttenuation/docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build examples
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.nim == '2.0.x' }}
+        shell: bash
+        run: |
+          cd xrayAttenuation/examples
+          nim c -d:musl -d:staticBuild -d:release calc_gas_mixtures.nim
+
+      - name: Upload example as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: calc_gas_mixtures
+          path: xrayAttenuation/examples/calc_gas_mixtures
+
+  release:
+    runs-on: ${{ matrix.os }}
+    needs: build
+    strategy:
+      fail-fast: false
+      matrix:
+        nim:
+          - '2.0.x'
+        os:
+          - ubuntu-latest
+    name: '${{ matrix.nim }} (${{ matrix.os }})'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          path: xrayAttenuation
+
+      - name: Download binary
+        uses: actions/download-artifact@v3
+        with:
+          name: calc_gas_mixtures
+          path: ./ # Specify the path to download the binary to
+
+      - name: Create GitHub Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          body: |
+            Release notes for version ${{ github.ref }}
+          draft: false
+          prerelease: false
+
+      - name: Upload Release Asset
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./calc_gas_mixtures
+          asset_name: calc_gas_mixtures
+          asset_content_type: application/octet-stream

examples/calc_gas_mixture_fractions.nim → examples/calc_gas_mixtures.nim

@@ -48,7 +48,48 @@ proc getMassFractions(gm: GasMixture): seq[(string, float)] =
       let fraction = cFrac * ratio * molarMass(c) / molarMass(gm)
       result.add (el, float fraction)
 
-proc gas(elements: seq[string], pressure: mbar, T = 293.15.K) =
+proc genOutfile(gm: GasMixture, outfile, outdir: string): string =
+  if outfile.len > 0: result = outfile
+  else:
+    if outdir.len > 0: result = outdir & "/"
+    result.add "transmission"
+    for el, frac in gm:
+      result.add &"_{el}_{frac}"
+    result.add &"_{gm.pressure}_{gm.temperature}"
+    result.add ".csv"
+
+proc calcTransmission(gm: GasMixture, length: cm, energyMin, energyMax: keV, num: int, outfile: string) =
+  let E = linspace(energyMin.float, energyMax.float, num)
+  let df = toDf({"Energy [keV]" : E})
+    .mutate(f{float: "Transmission" ~ transmission(gm, length, idx("Energy [keV]").keV).float})
+  df.writeCsv(outfile)
+
+proc calculateTransmissions(gm: GasMixture, length: cm, energyMin, energyMax: keV, num: int, outfile, outdir: string) =
+  ## Calculates the transmission of the combined gas mixture and all compounds (for their partial
+  ## pressure) and writes a CSV file to `outfile`.
+  let outfile = genOutfile(gm, outfile, outdir)
+  calcTransmission(gm, length, energyMin, energyMax, num, outfile)
+  # 2. split by individual compounds in gas
+  for el, frac in gm:
+    # calc partial pressure
+    let P = gm.pressure * frac
+    # construct helper gas mixture
+    let gmP = initGasMixture(gm.temperature, P, @[el], @[1.0])
+    let outfile = genOutfile(gmP, "", outdir) # always use autogenerated name for partial pressures
+    calcTransmission(gmP, length, energyMin, energyMax, num, outfile)
+
+proc gas(elements: seq[string], pressure: mbar, T = 293.15.K,
+         length = -1.cm, energyMin = 0.keV, energyMax = 15.keV, numEnergies = 1000,
+         outfile = "", outdir = "") =
+  ## Computes the particle fractions for each compound in the gas mixture. For each
+  ## compound it also prints the fraction split by mass fraction of the compound
+  ## (under 'Particle fractions'). And for 'Mass fractions' prints the mass fractions
+  ## of each element of the total masses.
+  ##
+  ## If a `length` is given in centimeter, it will also calculate the transmission of
+  ## of X-rays through such a gas in the energy range `[energyMin, energyMax]` and store
+  ## it `outfile`. In addition extra outfiles derived from `outfile` are produced for each
+  ## gas compound split by their partial pressures.
   var gases: seq[Compound]
   var frac: seq[float]
   for el in elements:
@@ -79,6 +120,9 @@ proc gas(elements: seq[string], pressure: mbar, T = 293.15.K) =
   for fr in getMassFractions(gm):
     stdout.styledWriteLine(fgRed, &"\t{fr[0]:<2}: {fr[1]}")
 
+  if length > 0.cm:
+    gm.calculateTransmissions(length, energyMin, energyMax, numEnergies, outfile, outdir)
+
 proc solid(elements: seq[string], ρ = -1.0.g•cm⁻³) =
   var elRT: seq[(ElementRT, int)]
   for el in elements:

examples/nim.cfg

@@ -0,0 +1,7 @@
+# From Chuck's nim.cfg
+@if musl:       # Statically links `foo` with musl; --opt:size trades more speed
+  cc            = gcc               # NOTE: This seems to work better as a ..
+  gcc.exe       = "musl-gcc"        #..per-module foo.nim.cfg than here.
+  gcc.linkerexe = "musl-gcc"
+  passL         = "-static -s"
+@end

xrayAttenuation.nimble

@@ -12,3 +12,13 @@ requires "ggplotnim >= 0.5.1"
 requires "unchained >= 0.1.9"
 requires "numericalnim"
 requires "cligen"
+
+task ciDeps, "Install CI dependencies":
+  exec "nimble install nimhdf5"
+
+task test, "Run the tests":
+  exec "nim c -r tests/tests.nim"
+  exec "nim c -r playground/mean_free_path.nim"
+  # only compile for now
+  ## Does not compile right now due to some weird nimhdf5 regression!
+  #exec "nim c playground/llnl_telescope_reflectivity.nim"