Bumped the version and added devpi documentation.

README.md

-# pes_to_spec
+# Virtual spectrometer
 
 The aim of this project is to read low-resolution photon spectrometer measurements and predict, with an uncertainty band, a high-resolution invasive
 photon spectrometer result, in such a way that one may continue to collect low-resolution data without stopping the beam, but obtaining nevertheless, high-resolution
@@ -10,17 +10,32 @@ The concept is to collect both results simultaneously during a training phase an
 
 One may install it simply with `pip install pes_to_spec`.
 
+While the dependencies should be automatically used, using the Intel-optimized `numpy` and `scipy` packages is recommended, as they are much faster.
+This has been tested with `scipy==1.7.3`, but it should work with any version of scipy and numpy.
+```
+# install the optimized numpy and scipy versions
+# skip dependencies
+pip install --force-reinstall -i https://pypi.anaconda.org/intel/simple --no-dependencies numpy scipy
+# now install dependencies
+pip install numpy scipy
+# install PyTorch
+pip install torch --index-url https://download.pytorch.org/whl/cpu
+```
+
 ## Usage
 
 The API may be used as follows:
 
 ```
 from pes_to_spec.model import Model
+from itertools import product
 
 # this is the main object holding all
 # information needed for training and prediction
 # the default parameters should be sufficient in most times
-model = Model()
+# if some channels are dead, you may want to specify the active channels
+channels = [f"channel_{i}_{l}" for i, l in product(range(1, 5), ["A", "B", "C", "D"])]
+model = Model(channels=channels)
 
 # this trains the model
 # low_resolution_raw_data is a dictionary with keys "channel_[1-4]_[A-D]" and values set to 2D-shaped
@@ -29,7 +44,8 @@ model = Model()
 # high_resolution_intensity and high_resolution_photon_energy are estimates from the high-resolution invasive spectrometer
 model.fit(low_resolution_raw_data,
           high_resolution_intensity,
-          high_resolution_photon_energy)
+          high_resolution_photon_energy,
+          pulse_energy=beam_intensity)
 
 # save it for later usage:
 model.save("model.joblib")
@@ -42,7 +58,7 @@ model = Model.load("model.joblib")
 # as before, the low_resolution_raw_data refers to a dictionary mapping the channel name
 # in the format "channel_[1-4]_[A-D]" to the 2D numpy array with shape (number_of_train_IDs, features)
 # all names and shapes must match the format in training, except for the number_of_train_IDs, which may vary
-interpolated_high_resolution_data = model.predict(low_resolution_raw_data)
+interpolated_high_resolution_data = model.predict(low_resolution_raw_data, pulse_energy=beam_intensity)
 
 # extra useful functions for debugging:
 
@@ -100,16 +116,3 @@ low_resolution_raw_data = {ch: run['SA3_XTD10_PES/ADC/1:network',
 
 After installation, the command-line tool `offline_analysis` may be used to test the tool in recorded datasets.
 
-## Exploration initial tests
-
-A first draft and explorative code can be seen in the `exploration` directory.
-
-1. inv_train.py -> Train a model on the specific RUN.
-Thish will save the pca model and fit model in experiments/YOUR_DIR/checkpoints and the data in 
-experiments/YOUR_DIR/data.
-
-2. inv_eval.py -> Use to evaluate the trained model
-
-3. inv_inference -> Use trained model to do inference on new data point
-
-4. data_drift_check.py  -> Check data drift between two datasets

Update_in_DA_server.md

+# Updating wheel in DA server
+
+This tool is packaged and made available through the DA server.
+The following commands can be used to update the tool in the DA server:
+
+```
+# if not done before:
+devpi use https://devpi.exfldadev01.desy.de/
+devpi login <username>
+devpi push --index euxfel/internal <my_file.whl>
+```
+
+# Installing it from the DA server
+
+To install this tool from the DA server, use the following index URL:
+
+```
+pip install --index-url "https://devpi.exfldadev01.desy.de/euxfel/internal" pes_to_spec==X.Y.Z
+```
+

pes_to_spec/__init__.py

@@ -2,4 +2,4 @@
 Estimate high-resolution photon spectrometer data from low-resolution non-invasive measurements.
 """
 
-VERSION = "0.2.7"
+VERSION = "0.2.8"