Fdmnes updates + fully migrate struct2xas from Larch

.github/workflows/test-ubuntu.yml

@@ -27,14 +27,13 @@ jobs:
           channel-priority: true
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.python-version }}
-      - name: Install conda dependencies
-        run: |
-          printenv
-          conda install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.26" scipy pytest pytest-cov coverage
+          auto-activate-base: false
+          mamba-version: "*"
+          use-mamba: true
       - name: Install larixite and dependencies with pip
         run: |
-          pip install ".[dev,test,doc]"
+          python -m pip install --upgrade pip
+          python -m pip install ".[all]"
       - name: Run test suite
         run: |
-          cd tests
-          python -m pytest --cov=./ --cov-report=xml
+          python -m pytest --cov=larixite --cov-report=xml

CHANGELOG.md

@@ -0,0 +1,35 @@
+# Changelog
+
+Notable changes to this project will be documented in this file. The GitHub
+Release Notes will also be useful.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+The versioning scheme followed is `YYYY.MAJOR.MINOR`:
+
+- `YYYY`: year of release
+- `MAJOR`: major feature (= change in API, no backward compatibility)
+- `MINOR`: minor feature (= bug fixes, minor changes not affecting the API, backward compatible)
+
+## [2026.1.0 - not released yet]
+
+### web application
+
+    - Separate FEFF and FDMNES sections for XAS input generation
+    - FDMNES: added optimization checkbox
+    - FDMNES: added Green formalism checkbox
+    - Added more tests
+
+### `fdmnes`
+
+    - Update to FDMNES version March 2026
+    - Add `make_sbatch` with a template for the ESRF SLURM scheduler
+    - Add `optimize : bool = False` option in `FdmnesXasInput` class to control if the input parameters are optimized (= more accurate calcuation, but slower) or not
+    - `write_input()` defaults to `$HOME/.larixite/fdmnes/{job_prefix}_{YYMMDD_HHMMSS}`
+
+### `struc2xas`
+
+    - Fully migrated from `larch.xrd.struc2xas` (and removed there)
+    - Make `struc2xas` *deprecated* and start refactoring
+

notebooks/workflow_fdmnes.ipynb → examples/fdmnes_xas_workflow.ipynb

@@ -9,8 +9,8 @@
     "\n",
     "- Author: Mauro Rovezzi\n",
     "- Contact: mauro.rovezzi@esrf.fr\n",
-    "- Status: in progress\n",
-    "- Last update: 2025-05-14"
+    "- Status: *in progress...*\n",
+    "- Last update: 2026-05-19"
    ]
   },
   {
@@ -48,7 +48,7 @@
     "\n",
     "abs = \"Zn\"  #: select the absorber\n",
     "\n",
-    "fdmnes_executable = \"/home/mauro/local/fdmnes_Linux_2024_11_14/fdmnes_Linux/fdmnes_linux64\"  #: path to fdmnes executable (TODO: set your own path)"
+    "fdmnes_executable = \"fdmnes\"  #: path to fdmnes executable (TODO: set your own path)"
    ]
   },
   {
@@ -130,7 +130,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "f = FdmnesXasInput(sg, absorber=abs, struct_type=\"crystal\", radius=5)\n",
+    "f = FdmnesXasInput(sg, absorber=abs, struct_type=\"crystal\", radius=5, erange=\"-5 0.5 10\", optimize=True)\n",
     "text = f.get_input()\n",
     "print(text)"
    ]
@@ -148,7 +148,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "outdir = f.write_input()"
+    "jobdir = f.write_input()"
    ]
   },
   {
@@ -157,7 +157,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! cd {outdir.as_posix()} && {fdmnes_executable}"
+    "f.write_sbatch()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! module purge && module load fdmnes && cd {jobdir.as_posix()} && {fdmnes_executable}\n"
    ]
   },
   {
@@ -180,7 +189,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "sloth2411",
+   "display_name": "sloth2507",
    "language": "python",
    "name": "python3"
   },
@@ -194,7 +203,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,