Refactoring to prepare for new distribution function approach

.github/workflows/test.yaml

@@ -1,41 +1,69 @@
 # This is a basic workflow to help you get started with Actions
 
-name: test
+name: cpu-tests
 
 # Controls when the action will run.
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   pull_request:
     branches:
       - main
-    types:
-      - opened
-      - synchronize
-      - ready_for_review
-
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  test-its:
-
+  test-tsadar-cpu:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.11
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.11
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          activate-environment: tsadar-cpu
+          environment-file: env.yml
+      - shell: bash -el {0}
+        run: |
+          pytest tests/
+
+  test-tsadar-gpu:
+    runs-on: "gpu_runner"
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.11
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          activate-environment: tsadar-gpu
+          environment-file: env_gpu.yml
+      - shell: bash -el {0}
+        run: |
+          pytest tests/
+
+
+      # - shell: bash -el {0}
+        # run: mamba env create -f env.yml
+    # steps:
+    # - uses: actions/checkout@v3
+    # - name: Set up Python 3.11
+    #   uses: actions/setup-python@v2
+    #   with:
+    #     python-version: 3.11
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install --upgrade black
-        python -m pip install --upgrade pytest wheel
-        python -m pip install --upgrade -r requirements.txt
+    # - name: Install dependencies
+    #   run: |
+    #     python -m pip install --upgrade pip
+    #     python -m pip install --upgrade black
+    #     python -m pip install --upgrade pytest wheel
+    # #     python -m pip install --upgrade -r requirements.txt
 
-    - name: Test with pytest
-      run: |
-        pytest tests/
+    #   - name: Test with pytest
+    #     run: |
+    #       python -m pip install pytest
+    #       CPU_ONLY=True pytest tests/

configs/1d/defaults.yaml

@@ -1,7 +1,5 @@
 parameters:
-    species1:
-        type:
-            electron:
+    electron:
         Te:
             val: .6
             active: False
@@ -12,31 +10,8 @@ parameters:
             active: False
             lb: 0.001
             ub: 1.0
-        m:
-            val: 3.0
-            active: False
-            lb: 2.0
-            ub: 5.0
-            matte: False
-        fe:
-            val: [ ]
-            active: False
-            length: 3999
-            type:
-                DLM:
-            lb: -100.
-            ub: -0.5
-            fe_decrease_strict: False
-            symmetric: False
-            dim: 1
-            v_res: 0.1
-            temp_asym: 1.0
-            m_theta: 0.0
-            m_asym: 1.
 
-    species2:
-        type:
-            ion:
+    ion-1:
         Ti:
             val: 0.12
             active: False
@@ -56,8 +31,6 @@ parameters:
             active: False
 
     general:
-        type:
-            general:
         amp1:
             val: 1.
             active: False
@@ -106,7 +79,8 @@ parameters:
 other:
     expandedions: False
     extraoptions:
-        load_ion_spec: False
+        spectype: 1d
+        load_ion_spec: false
         load_ele_spec: True
         fit_IAW: False
         fit_EPWb: True
@@ -115,6 +89,9 @@ other:
     PhysParams:
         background: [0, 0]
         norm: 0
+        widIRF: 
+            spect_stddev_ele: 1.3
+            spect_stddev_ion: 0.015
     iawoff: 0
     iawfilter: [1, 4, 24, 528]
     CCDsize: [1024, 1024]
@@ -158,7 +135,7 @@ data:
             pixel
         start: 400
         end: 600
-        skip: 10
+        skip: 50
     background:
         type:
             pixel
@@ -186,7 +163,7 @@ optimizer:
     x_norm: False
     grad_method: AD
     batch_size: 2
-    num_epochs: 1000
+    num_epochs: 120
     learning_rate: 1.0e-2
     parameter_norm: True
     refine_factor: 0
@@ -204,4 +181,4 @@ dist_fit:
 
 mlflow:
     experiment: inverse-thomson-scattering
-    run: base
+    run: new

configs/1d/inputs.yaml

@@ -1,8 +1,5 @@
 parameters:
-    species1:
-        type:
-            electron:
-            active: False
+    electron:
         Te:
             val: .5
             active: True
@@ -13,30 +10,23 @@ parameters:
             active: True
             lb: .001
             ub: 1.
-        m:
-            val: 3.0
-            active: True
-            lb: 2.
-            ub: 5.
         fe:
-            val: [ ]
-            active: False
-            length: 3999
-            type:
-                DLM:
-            lb: -100.
-            ub: -0.5
+            active: True
+            type: dlm
             dim: 1
-            v_res: 0.1
-    species2:
-        type:
-            ion:
-            active: False
+            nv: 64
+            params:
+                m:
+                    val: 2.5
+                    lb: 2.0
+                    ub: 5.0
+    ion-1:
         Ti:
             val: .2
             active: False
             lb: 0.01
             ub: 3.
+            same: False
         Z:
             val: 8.
             active: False
@@ -46,12 +36,9 @@ parameters:
             val: 40.
             active: False
         fract:
-            val: 1.0
+            val: 1.
             active: False
     general:
-        type:
-            general:
-            active: False
         amp1:
             val: 1.
             active: True
@@ -101,5 +88,5 @@ parameters:
 other:
     refit: False
     refit_thresh: 5.0
-    calc_sigmas: True
+    calc_sigmas: false