nested-fit 5.5.4__tar.gz → 5.6.0.dev106__tar.gz

nested_fit-5.6.0.dev106/.github/workflows/build_wheels.yml

@@ -0,0 +1,172 @@
+name: Python Build Wheels
+
+on:
+  push:
+    branches: ["master", "dev"]
+
+jobs:
+  build_wheels:
+    name: Build ${{ matrix.runs_on }} [${{ matrix.arch }}]
+    runs-on: ${{ matrix.runs_on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Run for linux x86_64, macos arm64 and macos x86_64
+        include:
+          - runs_on: macos-15-intel
+            arch: x86_64
+            # minver: "10.15"
+            minver: "15.0"
+          - runs_on: macos-latest
+            arch: arm64
+            # minver: "11.0"
+            minver: "15.0"
+          - runs_on: ubuntu-latest
+            arch: x86_64
+            minver: ""
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install build tools (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gfortran gcc cmake make
+
+      - name: Install llvm + libomp (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install llvm gcc libomp
+
+      # - name: Install conda (macOS)
+      #   if: runner.os == 'macOS'
+      #   uses: conda-incubator/setup-miniconda@v2
+      #   with:
+      #     miniforge-version: "latest"
+      #     activate-environment: buildenv
+      #     environment-file: ""
+      #     auto-activate-base: false
+      #
+      # - name: Install buildtools (macOS)
+      #   if: runner.os == 'macOS'
+      #   run: |
+      #     conda install -n buildenv -c conda-forge gfortran=11 libgfortran=5 libgcc libgfortran5 libcxx
+      #     echo "CONDA_BIN=$CONDA_PREFIX/bin" >> $GITHUB_ENV
+      #     echo "DYLD_FALLBACK_LIBRARY_PATH=$CONDA_PREFIX/lib" >> $GITHUB_ENV
+      #   shell: bash -l {0}
+
+      - name: Deploy pre-release
+        if: startsWith(github.ref, 'refs/heads/dev')
+        shell: bash
+        run: |
+          BASE_VERSION=$(python3 -c 'import tomllib; print(tomllib.load(open("pyproject.toml", "rb"))["project"]["version"])')
+          DEV_VERSION="${BASE_VERSION}.dev${GITHUB_RUN_NUMBER}"
+          if [[ "$RUNNER_OS" == "macOS" ]]; then sed -i '' "s/version = \".*\"/version = \"${DEV_VERSION}\"/" pyproject.toml; else sed -i "s/version = \".*\"/version = \"${DEV_VERSION}\"/" pyproject.toml; fi
+          echo "Dev version: ${DEV_VERSION}"
+
+      - name: Fix git interactivity (macOS)
+        if: runner.os == 'macOS'
+        shell: bash
+        run: |
+          echo "GIT_TERMINAL_PROMPT=0" >> $GITHUB_ENV
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
+          git rev-parse HEAD
+
+      - name: Build wheels (macOS)
+        if: runner.os == 'macOS'
+        uses: pypa/cibuildwheel@v3.0.1
+        env:
+          CIBW_ARCHS_MACOS: ${{ matrix.arch }}
+
+          # export DYLD_FALLBACK_LIBRARY_PATH=${{ env.DYLD_FALLBACK_LIBRARY_PATH }}
+          # echo "DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH"
+          CIBW_BEFORE_BUILD: |
+            python3 -c "import os,subprocess; print('pwd', os.getcwd()); subprocess.run(['git','rev-parse','HEAD'], check=True)"
+
+          # PATH="/usr/bin:/usr/local/bin:$PATH"
+          # SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
+          CIBW_ENVIRONMENT: >
+            MACOSX_DEPLOYMENT_TARGET=${{ matrix.minver }}
+            CMAKE_OSX_DEPLOYMENT_TARGET=${{ matrix.minver }}
+            CMAKE_OSX_ARCHITECTURES=${{ matrix.arch }}
+            CC=$(brew --prefix llvm)/bin/clang
+            CXX=$(brew --prefix llvm)/bin/clang++
+            FC=$(brew --prefix gcc)/bin/gfortran
+            GIT_TERMINAL_PROMPT=0
+        with:
+          package-dir: .
+          output-dir: wheelhouse
+          config-file: "{package}/pyproject.toml"
+
+      - name: Build wheels (Linux)
+        if: runner.os == 'Linux'
+        uses: pypa/cibuildwheel@v3.0.1
+        with:
+          package-dir: .
+          output-dir: wheelhouse
+          config-file: "{package}/pyproject.toml"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  make_sdist:
+    name: Make Python sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Deploy pre-release
+        if: startsWith(github.ref, 'refs/heads/dev')
+        shell: bash
+        run: |
+          BASE_VERSION=$(python3 -c 'import tomllib; print(tomllib.load(open("pyproject.toml", "rb"))["project"]["version"])')
+          DEV_VERSION="${BASE_VERSION}.dev${GITHUB_RUN_NUMBER}"
+          if [[ "$RUNNER_OS" == "macOS" ]]; then sed -i '' "s/version = \".*\"/version = \"${DEV_VERSION}\"/" pyproject.toml; else sed -i "s/version = \".*\"/version = \"${DEV_VERSION}\"/" pyproject.toml; fi
+          echo "Dev version: ${DEV_VERSION}"
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_to_index:
+    name: Upload to PyPI index
+    needs: [build_wheels, make_sdist]
+    environment: pypi
+
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Generate attestations
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # password: ${{ secrets.pypi_password }}
+          # repository-url: "https://pypi.org/legacy"
+          verbose: true
+          skip-existing: true
+          # attestations: false
+

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/CMakeLists.txt

@@ -2,16 +2,18 @@ cmake_minimum_required(VERSION 3.10)
 
 # NOTE: (César) : If we are on macOS set the minimum supported version to 10.15
 #				  due to C++17 support.
-if(APPLE)
-	set(CMAKE_OSX_DEPLOYMENT_TARGET "10.15" CACHE STRING "" FORCE)
-endif()
+# if(APPLE)
+# 	set(CMAKE_OSX_DEPLOYMENT_TARGET "10.15" CACHE STRING "" FORCE)
+# endif()
 
 # The nested_fit version being built -> This gets copied everywhere inside the project code
 # For more info see the 'src/Mod_metadata.f90.in' file
 # Read the version from the .toml file since this is what will be pushed to the repo
 file(READ "pyproject.toml" tomlfile)
-string(REGEX MATCH "version = \"([0-9]+\\.[0-9]+\\.[0-9]+)\"" vn ${tomlfile})
+string(REGEX MATCH "version[ \t]*=[ \t]*\"([0-9]+\.[0-9]+\.[0-9]+)(\.dev[0-9]+)?\"" vn ${tomlfile})
 set(project_version ${CMAKE_MATCH_1})
+message(STATUS "Build: ${CMAKE_MATCH_1}${CMAKE_MATCH_2}")
+set(dev_version "${CMAKE_MATCH_2}")
 
 # This is just for the clangd LSP
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -76,7 +78,7 @@ add_definitions("-D'PROFILED(x)'=''")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)
 
 # Set nested fit version strings
-set(nested_fit_version_full_str "${CMAKE_PROJECT_VERSION_MAJOR}.${CMAKE_PROJECT_VERSION_MINOR}.${CMAKE_PROJECT_VERSION_PATCH}")
+set(nested_fit_version_full_str "${CMAKE_PROJECT_VERSION_MAJOR}.${CMAKE_PROJECT_VERSION_MINOR}.${CMAKE_PROJECT_VERSION_PATCH}${dev_version}")
 set(nested_fit_version_str "${CMAKE_PROJECT_VERSION_MAJOR}.${CMAKE_PROJECT_VERSION_MINOR}")
 string(CONCAT nested_fit_target "nested_fit" ${nested_fit_version_full_str})
 string(REPLACE "." "_" nested_fit_target_ac ${nested_fit_target})
@@ -91,6 +93,7 @@ set(SRC_FILES_COMM
     src/Mod_likelihood.f90   
     src/Mod_potentials.f90
     src/Mod_integrated_func.f90
+    src/Mod_array_tries.f90
 
     src/USERFCN_2D.f90
     src/USERFCN_SET.f

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nested_fit
-Version: 5.5.4
+Version: 5.6.0.dev106
 Summary: The nested_fit package.
 Author: Martino Trassinelli, Lune Maillard, César Godinho
 Project-URL: Homepage, https://github.com/martinit18/nested_fit

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/README.md

@@ -161,6 +161,7 @@ For this purpose, the python module `nested_py` can be used also for compressed
 Together with this file, also the files `nf_output_points.paramnames` and `nf_output_points.ranges` are created for the use of GetDist and Anesthetic python libraries.
 - `nf_output_cluster_mean_std.dat`: contains the number of clusters, number of point per clusters, and mean and standard deviations for each cluster (if the clustering option is activated).
 - `nf_output_cluster_max.dat`: contains the number of clusters, the maximum value of the likelihood and the corresponding parameter values (if the clustering option is activated).
+- `nf_energy.txt`: contains the volume and energy associated to the discarded and final live points. For a quantum potential, the decomposition of the energy between the avergaed potential and the replicas interaction is also given, as well as the temperature. Only created when exploring potentials.
 
 **Details of the input file line by line**
 
@@ -169,14 +170,15 @@ A complete selection of input files example is given in the folder `examples` wh
 It follows a complete description of `nf_input.yaml` file.
 
 ```yaml
-version: 5.5                             # Program version
+version: 5.6                             # Program version
 calculation_mode: DATA                   # Type of calculation
 ```
 The type of calculation is spefified by `calculation_mode` variable. 
 Available options are:
 - `DATA`: for data analysis. A likelihood function is explored the Bayesian evidence is evaluated. It  requires a data file to read and thus the inputs `datafiles, specstr, likelihood`.
 - `INTEGRAL`: for the calculation of the integral of a given function.
-- `POTENTIAL`: for exploration of a potential energy and for building the partition function. 
+- `POTENTIAL`: for exploration of a classical potential energy and for building the partition function.
+- `Q_POTENTIAL`: for exploration of a quantum potential energy and for building the partition function. 
 
 ```yaml
 datafiles: file1.csv [, file2.csv, ...]  # Name of the data file(s)
@@ -232,7 +234,8 @@ search:
     max_tries: 1000     # Maximum tries before stop (max_tries * tries_mult)
     tries_mult: 100     # Max tries multiplier
     num_tries: 1        # Number of runs
-    max_steps: 100000   # Max number of steps before stop
+    hard_writing: true  # Write dead points on a temporary file
+    max_steps: 100000   # Max number of steps before stop (required if hard_writing false)
 ```
 
 For the moment there are, 
@@ -242,11 +245,14 @@ Except for the simplest researche, the detailed balance is maybe not respected b
 - A uniform search around each live point `UNIFORM`, 
 - Three versions of slice sampling: `SLICE_SAMPLING`, `SLICE_SAMPLING_TRANSF`,`SLICE_SAMPLING_ADAPT`.  The first two correspond, respectively, to the search being done in two different spaces (transformed and real) with the first one faster than the second one. `SLICE_SAMPLING_ADAPT` an adaptable step but the detailed balance is maybe not respected. 
 
-The first two parameters of the above line are specific to the search algorithm:
+`param1` and `param2` are specific to the search algorithm:
 - `RANDOM_WALK`,  `RANDOM_WALK_NO_DB` par. 1: fraction of standard deviation for each jump, par. 2: number of jumps. Suggested values: 0.1-0.2, 10-40. 
 -  `SLICE_SAMPLING`, `SLICE_SAMPLING_TRANSF`, and `SLICE_SAMPLING_ADAPT` par. 1: fraction of standard deviation for segment exploration, par. 2: number of jumps. Suggested values: ~1, 3-5. 
 - `UNIFORM` par. 1: fraction of standard deviation for the box size, par. 2: number of jumps. Suggested values: 0.1-1, 1.
 
+If `hard_writing` is true, the dead points are saved in the unformatted file `nf_output_dead_points_info.txt` during the run. The number of iterations is not limited and the content of the file is erased at the end of the run. Otherwise, the dead points are kept in memory during the run. In that case, the maximum number of iterations is given by `max_steps`. ATTENTION, if `writing: statistics` is false, the file  `nf_output_dead_points_info.txt` will not be written even if `search: hard_writing` is true.
+
+
 ```yaml
 convergence:
     method:    LIKE_ACC  # Method used for convergence 
@@ -281,6 +287,16 @@ For the second option:
 - `s`: agglomerative clustering with single linkage (par. 1: distance limit)
 - `k`: k nearest neighbours (no parameters)
 
+```yaml
+writing:
+    statistics:     true  # Calculate parameter statistics
+    all_parameters: true  # Write nf_output_points (big) file
+```
+
+These options allows to choose what is written in the ouput files:
+- `statistics`: if true, the mean, standard deviation, median and confidence levels of the parameters are computed and written in the `nf_output_res` files. ATTENTION, in that case, an array is created with all the points found during the run. ATTENTION, if `writing: all_parameters` is false and `search: hard_writing` is true, `writing: statistics` will be force set to FALSE if it is not.
+- `all_parameters`: if true, the `nf_output_points` files are written. ATTENTION, if false, the file  `nf_output_dead_points_info.txt` will not be written even if `search: hard_writing` is true.
+
 
 ## Function definition
 
@@ -375,20 +391,23 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 ## Present version and history of the past versions
 
-The present version is 5.5.4\
+The present version is 5.6.0\
 New features:
-- Add PyPI binary distribution for x86_64 macOS
-- Add PyPI binary distribution for multiple linux systems
-- Add PyPI source distribution as a default for other systems
-- Rename CLI command to `nested_fit` to use the latest installed version via pip
+- Optional management of memory of dead points (in RAM or file)
+- Optional writing of dead points information
+- Optional writing of parameter statistics (mean, standard deviation, etc.)
 
 
 Previous versions are:
+- 5.5 New RANDOM_WALK function with detailed balance respected \
+Add PyPI binary distribution for x86_64 macOS\
+Add PyPI binary distribution for multiple linux systems\
+Add PyPI source distribution as a default for other systems\
+Rename CLI command to `nested_fit` to use the latest installed version via pip\
  - 5.4 Merge of executable for data analysis and function exploration via the new calculation mode variable \
 Debug of not-yet  working feature of the version 5 compared to the version 4 \
-New outputs with maxima of each cluster \
-New RANDOM_WALK function with detailed balance respected
- - 5.3 New jupyter notebooks running in Google Colab \
+New outputs with maxima of each cluster 
+- 5.3 New jupyter notebooks running in Google Colab \
 New innterpolation functions in python library \
 Live display when sampling from python. Works in console and jupyter notebooks \
 Live display featured maximum likelihood prediction plot \

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/STEPBYSTEP_INSTALL.md

@@ -3,7 +3,7 @@
 ## For Mac OS
 1) If you do not have a fortran compiler installed, install homebrew from [https://brew.sh/](https://brew.sh/)\
 Then in a terminal install with homebrew the required components:\
- `brew install gcc g++ gfortran make cmake`
+ `brew install gcc gfortran make cmake`
 
 If you did not do it yet, add homebrew binary directory in the shell variable `PATH` by adding **IN THIS ORDER** in `.bashrc`: 
 ```sh

nested_fit-5.6.0.dev106/examples/README.md

@@ -0,0 +1,24 @@
+# Small guide of the examples
+
+ Examples of nested fit input files for data analysis are presented in the folder `data_analysis`. In particular
+- in `01_simple_example` is the **simples** example anyone can start for testing the program,
+- in `02_error_bars_data` an example is given for data with error bars and assuming a Gaussian probability for them, 
+- in `03_with_cluster_analysis` different cluster analyses are presented,
+- in `04_set_of_datafile` an example of **simultaneous analysis of set data files** is given,
+- in `05_data_2D` an example of **2D data** is given,
+- in `06_interpolation_function` the interpolation method is presented  (in a Jupyter notebook for practical reasons)
+
+Examples of nested fit input files for function exploration are presented in the folder `function_integration`: a Gaussian function in 5D `07_func_GAUSS` (the integral is 1 -> 0 in log) and a eggbox function for testing the clustering abilities `08_func_EGGBOX`.
+
+Examples of nested fit input files for potential exploration and analysis of the **partition function** with a choice of minimum temperature is given in the folder `potential_exploration`. Two Lennard-Jones clusters are given as example: a cluster with 7 classic atoms (`09_ENERGY_HARM_3D`) and a cluster with 3 atoms with nuclear quantum effects emulated with two replicas (`10_Q_ENERGY_HARM_3D`).
+
+
+Examples of use of the python library `nested_res.py` are presented in two jupyter notebooks
+- `simple_analysis_visu.ipynb` for a basic analysis and visualization of `nested_fit` outputs for a single analysis.
+- `simple_visualisation.ipynb` for basic visualisation of already computed analyses.
+- `set_of_files_analysis.ipynb` for the analysis of two spectra at the same time with two different, but correlated, functions.
+- `pandas_extended_analysis.ipynb` for a more **complex analysis** for different choice of model, conditions or data set. Here, the output results are collected in a unique pandas dataframe to be easily compared and visualized 
+
+Another notebook can be found in `examples/data_analysis/06_interpolation_function/pynf_interp.ipynb` for interpolation of external data.
+
+Numbered folders are referring to reference test benchmarks used to develop the code.

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/01_simple_example/RANDOM_WALK/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat     # Name of the data file
 specstr:    x,c              # Datafile layout
@@ -22,8 +22,8 @@ search:
   param2:     20                 # Param 2 of chosen method (see below)
   max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
   tries_mult: 100                # Max tries multiplier
-  # num_tries:  1                  # Number of runs
-  max_steps:  100000             # Max number of steps before stop
+  # num_tries:  1                # Number of runs
+  # max_steps:  100000           # Max number of steps before stop (required if hard_writing false)
 
 convergence:
   method:    LIKE_ACC            # Method used for convergence 

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/01_simple_example/RANDOM_WALK_NO_DB/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat     # Name of the data file
 specstr:    x,c              # Datafile layout
@@ -22,8 +22,8 @@ search:
   param2:     20                 # Param 2 of chosen method (see below)
   max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
   tries_mult: 100                # Max tries multiplier
-  # num_tries:  1                  # Number of runs
-  max_steps:  100000             # Max number of steps before stop
+  # num_tries:  1                # Number of runs
+  # max_steps:  100000           # Max number of steps before stop (required if hard_writing false)
 
 convergence:
   method:    LIKE_ACC            # Method used for convergence 

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/01_simple_example/RANDOM_WALK_SYN/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat     # Name of the data file
 specstr:    x,c              # Datafile layout
@@ -22,8 +22,8 @@ search:
   param2:     20                 # Param 2 of chosen method (see below)
   max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
   tries_mult: 100                # Max tries multiplier
-  # num_tries:  1                  # Number of runs
-  max_steps:  100000             # Max number of steps before stop
+  # num_tries:  1                # Number of runs
+  # max_steps:  100000           # Max number of steps before stop (required if hard_writing false)
 
 convergence:
   method:    LIKE_ACC            # Method used for convergence 

{nested_fit-5.5.4/examples/data_analysis/01_simple_example/internal_func_input → nested_fit-5.6.0.dev106/examples/data_analysis/01_simple_example/internal_func_hard_writing}/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat     # Name of the data file
 specstr:    x,c              # Datafile layout
@@ -22,8 +22,9 @@ search:
   param2:     3                  # Param 2 of chosen method (see below)
   max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
   tries_mult: 100                # Max tries multiplier
-  # num_tries:  1                  # Number of runs
-  max_steps:  100000             # Max number of steps before stop
+  num_tries:  10                 # Number of runs
+  hard_writing: true             # Write dead points on a temporary file
+  # max_steps:  100000           # Max number of steps before stop (required if hard_writing false)
 
 convergence:
   method:    LIKE_ACC            # Method used for convergence 

nested_fit-5.6.0.dev106/examples/data_analysis/01_simple_example/internal_func_input/nf_input.yaml

@@ -0,0 +1,41 @@
+version:    5.6              # Program version
+calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
+datafiles:  he-histo.dat     # Name of the data file
+specstr:    x,c              # Datafile layout
+# filefmt: .tsv              # (optional) for data separated by spaces or tabs
+# likelihood: GAUSSIAN       # (for data with error bars only) Name of the likelihood function
+
+function:
+  expression: gauss_bg(x, A, x_0, s, b_g) = \texttt{GAUSS_IF}(x, x_0, A, s) + b_g # function expression using an internal function in functions/internal_function.f90
+  params:                    # Parameters boundaries and co.
+    b_g:  { value: 0.11,    step: -1, min: 0,      max: 0.5}
+    x_0:  { value: 450,     step: -1, min: 400,    max: 600}
+    A:    { value: 300,     step: -1, min: 20,     max: 1000}
+    s:    { value: 20.0,    step: -1, min: 0,      max: 100}
+
+data: { xmin: 1, xmax: 1024, ymin: 0, ymax: 0 }    # Boundaries of data
+
+search:
+  livepoints: 1000               # Number of live points
+  method:     SLICE_SAMPLING     # Search method
+  param1:     1                  # Param 1 of chosen method (see below)
+  param2:     3                  # Param 2 of chosen method (see below)
+  max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
+  tries_mult: 100                # Max tries multiplier
+  num_tries:  1                  # Number of runs
+  hard_writing: false            # Write dead points on a temporary file
+  max_steps:  100000             # Max number of steps before stop (required if hard_writing false)
+
+convergence:
+  method:    LIKE_ACC            # Method used for convergence 
+  accuracy:  1.E-05              # Evidence final accuracy (in this case)
+
+# clustering:
+  # enabled:   true
+  # method:    k
+  # parameter1:  0.5
+  # parameter2: 0.2
+
+writing:
+    statistics:     true  # Calculate parameter statistics
+    all_parameters: true  # Write nf_ouptut_points (big) file

nested_fit-5.6.0.dev106/examples/data_analysis/01_simple_example/internal_func_no_points_file/nf_input.yaml

@@ -0,0 +1,41 @@
+version:    5.6              # Program version
+calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
+datafiles:  he-histo.dat     # Name of the data file
+specstr:    x,c              # Datafile layout
+# filefmt: .tsv              # (optional) for data separated by spaces or tabs
+# likelihood: GAUSSIAN       # (for data with error bars only) Name of the likelihood function
+
+function:
+  expression: gauss_bg(x, A, x_0, s, b_g) = \texttt{GAUSS_IF}(x, x_0, A, s) + b_g # function expression using an internal function in functions/internal_function.f90
+  params:                    # Parameters boundaries and co.
+    b_g:  { value: 0.11,    step: -1, min: 0,      max: 0.5}
+    x_0:  { value: 450,     step: -1, min: 400,    max: 600}
+    A:    { value: 300,     step: -1, min: 20,     max: 1000}
+    s:    { value: 20.0,    step: -1, min: 0,      max: 100}
+
+data: { xmin: 1, xmax: 1024, ymin: 0, ymax: 0 }    # Boundaries of data
+
+search:
+  livepoints: 1000               # Number of live points
+  method:     SLICE_SAMPLING     # Search method
+  param1:     1                  # Param 1 of chosen method (see below)
+  param2:     3                  # Param 2 of chosen method (see below)
+  max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
+  tries_mult: 100                # Max tries multiplier
+  num_tries:  1                  # Number of runs
+  hard_writing: false            # Write dead points on a temporary file
+  max_steps:  100000             # Max number of steps before stop (required if hard_writing false)
+
+convergence:
+  method:    LIKE_ACC            # Method used for convergence 
+  accuracy:  1.E-05              # Evidence final accuracy (in this case)
+
+# clustering:
+  # enabled:   true
+  # method:    k
+  # parameter1:  0.5
+  # parameter2: 0.2
+
+writing:
+    statistics:     true  # Calculate parameter statistics
+    all_parameters: false # Write nf_output_points (big) file

nested_fit-5.6.0.dev106/examples/data_analysis/01_simple_example/internal_func_no_stat/nf_input.yaml

@@ -0,0 +1,41 @@
+version:    5.6              # Program version
+calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
+datafiles:  he-histo.dat     # Name of the data file
+specstr:    x,c              # Datafile layout
+# filefmt: .tsv              # (optional) for data separated by spaces or tabs
+# likelihood: GAUSSIAN       # (for data with error bars only) Name of the likelihood function
+
+function:
+  expression: gauss_bg(x, A, x_0, s, b_g) = \texttt{GAUSS_IF}(x, x_0, A, s) + b_g # function expression using an internal function in functions/internal_function.f90
+  params:                    # Parameters boundaries and co.
+    b_g:  { value: 0.11,    step: -1, min: 0,      max: 0.5}
+    x_0:  { value: 450,     step: -1, min: 400,    max: 600}
+    A:    { value: 300,     step: -1, min: 20,     max: 1000}
+    s:    { value: 20.0,    step: -1, min: 0,      max: 100}
+
+data: { xmin: 1, xmax: 1024, ymin: 0, ymax: 0 }    # Boundaries of data
+
+search:
+  livepoints: 1000               # Number of live points
+  method:     SLICE_SAMPLING     # Search method
+  param1:     1                  # Param 1 of chosen method (see below)
+  param2:     3                  # Param 2 of chosen method (see below)
+  max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
+  tries_mult: 100                # Max tries multiplier
+  num_tries:  1                  # Number of runs
+  hard_writing: false            # Write dead points on a temporary file
+  max_steps:  100000             # Max number of steps before stop (required if hard_writing false)
+
+convergence:
+  method:    LIKE_ACC            # Method used for convergence 
+  accuracy:  1.E-05              # Evidence final accuracy (in this case)
+
+# clustering:
+  # enabled:   true
+  # method:    k
+  # parameter1:  0.5
+  # parameter2: 0.2
+
+writing:
+    statistics:     false # Calculate parameter statistics
+    all_parameters: true  # Write nf_output_points (big) file

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/01_simple_example/latex_func_input/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat     # Name of the data file
 specstr:    x,c              # Datafile layout
@@ -22,8 +22,8 @@ search:
   param2:     3                  # Param 2 of chosen method (see below)
   max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
   tries_mult: 100                # Max tries multiplier
-  # num_tries:  1                  # Number of runs
-  max_steps:  100000             # Max number of steps before stop
+  # num_tries:  1                # Number of runs
+  # max_steps:  100000           # Max number of steps before stop (required if hard_writing false)
 
 convergence:
   method:    LIKE_ACC            # Method used for convergence 

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/01_simple_example/legacy_func_input/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat     # Name of the data file
 specstr:    x,c              # Datafile layout
@@ -22,8 +22,8 @@ search:
   param2:     3                  # Param 2 of chosen method (see below)
   max_tries:  1000               # Maximum tries before stop (max_tries * tries_mult)
   tries_mult: 100                # Max tries multiplier
-  # num_tries:  1                  # Number of runs
-  max_steps:  100000             # Max number of steps before stop
+  # num_tries:  1                # Number of runs
+  # max_steps:  100000           # Max number of steps before stop (required if hard_writing false)
 
 convergence:
   method:    LIKE_ACC            # Method used for convergence 

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/02_error_bars_data/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  eb_gauss_bg-x0_300-sigma_20-A_20000-p_to_bg_0.05-bin_1.dat
 #specstr:    x,c,ce

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/03_with_cluster_analysis/DBSCAN-RANDOM_WALK_SYN/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat
 #specstr:    x,c,ce

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/03_with_cluster_analysis/DBSCAN-SLICE_SAMPLING/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat
 #specstr:    x,c,ce

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/03_with_cluster_analysis/KNN-RANDOM_WALK_SYN/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat
 #specstr:    x,c,ce

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/03_with_cluster_analysis/KNN-SLICE_SAMPLING/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat
 #specstr:    x,c,ce

{nested_fit-5.5.4 → nested_fit-5.6.0.dev106}/examples/data_analysis/03_with_cluster_analysis/agglomerative-RANDOM_WALK_SYN/nf_input.yaml

@@ -1,4 +1,4 @@
-version:    5.5              # Program version
+version:    5.6              # Program version
 calculation_mode: DATA       # Type of calculation (DATA for data, POTENTIAL for potential landscapes, INTEGRAL for function integrals)
 datafiles:  he-histo.dat
 #specstr:    x,c,ce