✨ Add case studies (#1)

This adds the case studies as is from the "capsule 20230218" email correspondence with some cleanup and additional tooling.

.github/workflows/test.yml

@@ -0,0 +1,45 @@
+name: Tests
+
+on:
+  # For now commented out since private repositories only have a limited amount of CI time
+  # push:
+  # pull_request:
+  workflow_dispatch:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Run pre-commit
+        uses: pre-commit/action@v3.0.0
+
+  test:
+    name: Run ${{ matrix.case_study }}
+    runs-on: ubuntu-latest
+    needs: [pre-commit]
+    strategy:
+      matrix:
+        case_study: [4TT, dPSI, rc]
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+      - name: Set up Python "3.10"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          python -m pip install -r requirements.txt
+      - name: Show installed packages
+        run: python -m pip freeze
+      - name: Run tests
+        run: |
+          python -m pytest ${{ matrix.case_study }}

.gitignore

@@ -127,3 +127,14 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# vscode config
+.vscode
+
+# result folders
+20*/
+results/
+guide/
+
+# Corrected 4TT data generate after the first analysis step
+4TT/data/corr4TT.ascii

.pre-commit-config.yaml

@@ -0,0 +1,57 @@
+ci:
+  skip: [interrogate]
+
+default_language_version:
+  python: python3.10
+
+repos:
+  # Formatters
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: debug-statements
+      - id: fix-encoding-pragma
+        args: [--remove]
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.4 # Use the sha or tag you want to point at
+    hooks:
+      - id: prettier
+
+  # Notebook tools
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        args:
+          - "--drop-empty-cells"
+          - "--extra-keys"
+          - "metadata.vscode metadata.language_info.version"
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.6.1
+    hooks:
+      - id: nbqa-black
+        additional_dependencies: [black==23.1.0]
+        args: [--nbqa-mutate]
+      - id: nbqa-pyupgrade
+        additional_dependencies: [pyupgrade==3.3.1]
+        args: [--nbqa-mutate, --py310-plus]
+      - id: nbqa-flake8
+      - id: nbqa-check-ast
+      - id: nbqa-isort
+        additional_dependencies: [isort==5.12.0]
+        args: [--nbqa-mutate]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.2
+    hooks:
+      - id: codespell
+        types: [file]
+        types_or: [python, pyi, markdown, rst, jupyter]
+        args: [-L doas]

4TT/models/model.yml

@@ -0,0 +1,49 @@
+# type: doas
+
+initial_concentration:
+  j1:
+    compartments: [S2, S1, T1, S2rel, T1hot]
+    parameters: [j.1, j.0, j.0, j.0, j.0]
+
+k_matrix:
+  k1:
+    matrix:
+      "(S2rel, S2)": kinetic.to_S2rel_from_S2
+      "(S1, S2)": kinetic.to_S1_from_S2
+      "(S1, S2rel)": kinetic.to_S1_from_S2rel
+      "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
+      "(T1hot, S1)": kinetic.to_T1hot_from_S1
+      "(T1, T1hot)": kinetic.to_T1_from_T1hot
+      "(T1, T1)": kinetic.from_T1
+
+megacomplex:
+  doas:
+    type: damped-oscillation
+    labels: [osc1, osc2, osc3, osc4]
+    frequencies: [osc.freq.1, osc.freq.2, osc.freq.3, osc.freq.4]
+    rates: [osc.rates.1, osc.rates.2, osc.rates.3, osc.rates.4]
+  decay:
+    type: decay
+    k_matrix: [k1]
+  #  baseline:
+  #    type: baseline
+  #    dimension: time
+  artifact:
+    type: coherent-artifact
+    order: 3
+    width: artifact.CAwidth
+
+irf:
+  irf1:
+    type: spectral-gaussian
+    center: irf.center
+    width: irf.width
+    dispersion_center: irf.dispcenter
+    center_dispersion_coefficients: [irf.disp1, irf.disp2, irf.disp3]
+    model_dispersion_with_wavenumber: true
+
+dataset:
+  dataset1:
+    initial_concentration: j1
+    megacomplex: [doas, decay, artifact]
+    irf: irf1

4TT/models/model_refined6osc.yml

@@ -0,0 +1,58 @@
+# type: doas
+
+initial_concentration:
+  j1:
+    compartments: [S2, S1, T1, S2rel, T1hot]
+    parameters: [j.1, j.0, j.0, j.0, j.0]
+
+k_matrix:
+  k1:
+    matrix:
+      "(S2rel, S2)": kinetic.to_S2rel_from_S2
+      "(S1, S2)": kinetic.to_S1_from_S2
+      "(S1, S2rel)": kinetic.to_S1_from_S2rel
+      "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
+      "(T1hot, S1)": kinetic.to_T1hot_from_S1
+      "(T1, T1hot)": kinetic.to_T1_from_T1hot
+      "(T1, T1)": kinetic.from_T1
+
+megacomplex:
+  doas:
+    type: damped-oscillation
+    labels: [osc1, osc2, osc3, osc4, osc5, osc6]
+    frequencies:
+      [osc.freq.1, osc.freq.2, osc.freq.3, osc.freq.4, osc.freq.5, osc.freq.6]
+    rates:
+      [
+        osc.rates.1,
+        osc.rates.2,
+        osc.rates.3,
+        osc.rates.4,
+        osc.rates.5,
+        osc.rates.6,
+      ]
+  decay:
+    type: decay
+    k_matrix: [k1]
+  #  baseline:
+  #    type: baseline
+  #    dimension: time
+  artifact:
+    type: coherent-artifact
+    order: 3
+    width: artifact.CAwidth
+
+irf:
+  irf1:
+    type: spectral-gaussian
+    center: irf.center
+    width: irf.width
+    dispersion_center: irf.dispcenter
+    center_dispersion_coefficients: [irf.disp1, irf.disp2, irf.disp3]
+    model_dispersion_with_wavenumber: true
+
+dataset:
+  4TT:
+    initial_concentration: j1
+    megacomplex: [doas, decay, artifact]
+    irf: irf1

4TT/models/model_sequential.yml

@@ -0,0 +1,52 @@
+# type: doas
+
+initial_concentration:
+  j1:
+    # compartments: [S2, S1, T1, S2rel, T1hot]
+    # parameters: [j.1, j.0, j.0, j.0, j.0]
+    compartments: [S2, S1, T1, T1hot]
+    parameters: [j.1, j.0, j.0, j.0]
+
+k_matrix:
+  k1:
+    matrix:
+      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
+      "(S1, S2)": kinetic.to_S1_from_S2
+      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
+      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
+      "(T1hot, S1)": kinetic.to_T1hot_from_S1
+      "(T1, T1hot)": kinetic.to_T1_from_T1hot
+      "(T1, T1)": kinetic.from_T1
+
+megacomplex:
+  doas:
+    type: damped-oscillation
+    labels: [osc1, osc2, osc3, osc4]
+    frequencies: [osc.freq.1, osc.freq.2, osc.freq.3, osc.freq.4]
+    rates: [osc.rates.1, osc.rates.2, osc.rates.3, osc.rates.4]
+  decay:
+    type: decay
+    k_matrix: [k1]
+  #  baseline:
+  #    type: baseline
+  #    dimension: time
+  artifact:
+    type: coherent-artifact
+    order: 3
+    width: artifact.CAwidth
+
+irf:
+  irf1:
+    type: spectral-gaussian
+    center: irf.center
+    width: irf.width
+    dispersion_center: irf.dispcenter
+    center_dispersion_coefficients: [irf.disp1, irf.disp2, irf.disp3]
+    model_dispersion_with_wavenumber: true
+
+dataset:
+  # dataset1:
+  4TT:
+    initial_concentration: j1
+    megacomplex: [doas, decay, artifact]
+    irf: irf1

4TT/models/model_sequential5osc.yml

@@ -0,0 +1,51 @@
+# type: doas
+
+initial_concentration:
+  j1:
+    # compartments: [S2, S1, T1, S2rel, T1hot]
+    # parameters: [j.1, j.0, j.0, j.0, j.0]
+    compartments: [S2, S1, T1, T1hot]
+    parameters: [j.1, j.0, j.0, j.0]
+
+k_matrix:
+  k1:
+    matrix:
+      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
+      "(S1, S2)": kinetic.to_S1_from_S2
+      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
+      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
+      "(T1hot, S1)": kinetic.to_T1hot_from_S1
+      "(T1, T1hot)": kinetic.to_T1_from_T1hot
+      "(T1, T1)": kinetic.from_T1
+
+megacomplex:
+  doas:
+    type: damped-oscillation
+    labels: [osc1, osc2, osc3, osc4, osc5]
+    frequencies: [osc.freq.1, osc.freq.2, osc.freq.3, osc.freq.4, osc.freq.5]
+    rates: [osc.rates.1, osc.rates.2, osc.rates.3, osc.rates.4, osc.rates.5]
+  decay:
+    type: decay
+    k_matrix: [k1]
+  #  baseline:
+  #    type: baseline
+  #    dimension: time
+  artifact:
+    type: coherent-artifact
+    order: 3
+    width: artifact.CAwidth
+
+irf:
+  irf1:
+    type: spectral-gaussian
+    center: irf.center
+    width: irf.width
+    dispersion_center: irf.dispcenter
+    center_dispersion_coefficients: [irf.disp1, irf.disp2, irf.disp3]
+    model_dispersion_with_wavenumber: true
+
+dataset:
+  dataset1:
+    initial_concentration: j1
+    megacomplex: [doas, decay, artifact]
+    irf: irf1

4TT/models/model_sequential6osc.yml

@@ -0,0 +1,61 @@
+# type: doas
+
+initial_concentration:
+  j1:
+    # compartments: [S2, S1, T1, S2rel, T1hot]
+    # parameters: [j.1, j.0, j.0, j.0, j.0]
+    compartments: [S2, S1, T1, T1hot]
+    parameters: [j.1, j.0, j.0, j.0]
+
+k_matrix:
+  k1:
+    matrix:
+      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
+      "(S1, S2)": kinetic.to_S1_from_S2
+      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
+      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
+      "(T1hot, S1)": kinetic.to_T1hot_from_S1
+      "(T1, T1hot)": kinetic.to_T1_from_T1hot
+      "(T1, T1)": kinetic.from_T1
+
+megacomplex:
+  doas:
+    type: damped-oscillation
+    labels: [osc1, osc2, osc3, osc4, osc5, osc6]
+    frequencies:
+      [osc.freq.1, osc.freq.2, osc.freq.3, osc.freq.4, osc.freq.5, osc.freq.6]
+    rates:
+      [
+        osc.rates.1,
+        osc.rates.2,
+        osc.rates.3,
+        osc.rates.4,
+        osc.rates.5,
+        osc.rates.6,
+      ]
+  decay:
+    type: decay
+    k_matrix: [k1]
+  #  baseline:
+  #    type: baseline
+  #    dimension: time
+  artifact:
+    type: coherent-artifact
+    order: 3
+    width: artifact.CAwidth
+
+irf:
+  irf1:
+    type: spectral-gaussian
+    center: irf.center
+    width: irf.width
+    dispersion_center: irf.dispcenter
+    center_dispersion_coefficients: [irf.disp1, irf.disp2, irf.disp3]
+    model_dispersion_with_wavenumber: true
+
+dataset:
+  # dataset1:
+  4TT:
+    initial_concentration: j1
+    megacomplex: [doas, decay, artifact]
+    irf: irf1