From cd06da8c8b5f2877ee779fac2d73704b820fd8ae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= <devel@sciunto.org>
Date: Wed, 25 Jun 2025 11:48:48 +0200
Subject: [PATCH 1/4] add test

---
 tests/test_thickness.py | 67 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 tests/test_thickness.py

diff --git a/tests/test_thickness.py b/tests/test_thickness.py
new file mode 100644
index 0000000..068b7ed
--- /dev/null
+++ b/tests/test_thickness.py
@@ -0,0 +1,67 @@
+import pytest
+import yaml
+from pathlib import Path
+import os.path
+
+import numpy as np
+from numpy.testing import assert_allclose
+from numpy.testing import assert_almost_equal
+
+from optifik.minmax import thickness_from_minmax
+from optifik.analysis import smooth_intensities
+from optifik.io import load_spectrum
+
+
+def load():
+    test_data_dir = Path(__file__).parent.parent / 'data'
+    FOLDER = test_data_dir / 'spectraLorene' / 'sample1'
+
+    yaml_file = os.path.join(FOLDER, 'sample1.yaml')
+    with open(yaml_file, "r") as yaml_file:
+        thickness_dict = yaml.safe_load(yaml_file)
+    #print(thickness_dict)
+    data = [(os.path.join(FOLDER, fn), val) for fn, val in thickness_dict['known_thicknesses'].items()]
+    return data
+
+
+def test_minmax_sample1():
+    min_peak_prominence = 0.02
+    min_peak_distance = 10
+    skipped = ('011137.xy',
+               '012426.xy',
+               '012795.xy',
+               '012979.xy',
+               '011321.xy', #Insufficient number of data points
+               )
+
+    for path, expected in load():
+        file = os.path.split(path)[-1]
+        if file not in skipped:
+            lambdas, raw_intensities = load_spectrum(path, wavelength_min=450)
+            smoothed_intensities = smooth_intensities(raw_intensities)
+            r_index = 1.33 #TODO
+
+            prominence = 0.02
+            distance = 10
+
+            result = thickness_from_minmax(lambdas,
+                                           smoothed_intensities,
+                                           refractive_index=r_index,
+                                           min_peak_prominence=prominence,
+                                           min_peak_distance=distance,
+                                           method='ransac',
+                                           plot=False)
+
+            assert_allclose(result.thickness, expected, rtol=2.3e-1)
+
+#def test_fft_sample1():
+#    for name, value in known_values.sample1['known_thicknesses'].items():
+#        index = known_values.sample1['refractive_index']
+#        # this method works only for large thicknesses
+#        if value < 3000:
+#            continue
+#        path = os.path.join('spectra', name)
+#        lambdas, intensities = io.load_spectrum(path, lambda_min=450)
+#        result = thickness_from_fft(lambdas, intensities, refractive_index=index,)
+#        error = 100 * np.abs(result.thickness - value) / value
+#        assert(error < 5)

From 28077e2853b184e02c30b6d6a87a0ae684deafe7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= <devel@sciunto.org>
Date: Wed, 25 Jun 2025 11:48:59 +0200
Subject: [PATCH 2/4] add licence

---
 CHANGELOG.md   | 4 ++++
 README.md      | 6 ++++++
 pyproject.toml | 2 +-
 3 files changed, 11 insertions(+), 1 deletion(-)
 create mode 100644 CHANGELOG.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..65b2eeb
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,4 @@
+
+# x.x.x
+
+First version
diff --git a/README.md b/README.md
index be6680a..b07face 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 # Optifik
 
+TODO: write a paragraph here...
+
 
 This library replaces oospectro.
 
@@ -48,3 +50,7 @@ cd docs
 make html
 ```
 
+## Licence
+
+The source code is released under the GNU General Public License v3.0.
+See LICENSE for details.
diff --git a/pyproject.toml b/pyproject.toml
index d05cb02..e53c231 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ authors = [
   { name = "François Boulogne", email = "francois.boulogne@cnrs.fr" },
   { name = "Victor Ziapkoff", email = "victor.ziapkoff@universite-paris-saclay.fr" },
 ]
-license = "GPL-3.0-or-later"
+license = "GPL-3.0"
 readme = "README.md"
 requires-python = ">=3.13"
 dependencies = [

From 99bbb51fc14ce1020d4c43ceab307f99a695fb85 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= <devel@sciunto.org>
Date: Wed, 25 Jun 2025 11:49:20 +0200
Subject: [PATCH 3/4] add gitignore

---
 .gitignore | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..3547ba4
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+__pycache__
+.backups
+optifik.egg-info
+*.bak
+*.pyc
+.ipynb_checkpoints
+build/
+dist/

From 481f15ef7a30305febfa028b76a482a33498f619 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= <devel@sciunto.org>
Date: Wed, 25 Jun 2025 11:50:10 +0200
Subject: [PATCH 4/4] populate git ignore

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 3547ba4..1f811a3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,5 +4,7 @@ optifik.egg-info
 *.bak
 *.pyc
 .ipynb_checkpoints
+.venv
 build/
+_build/
 dist/