MAINT: organize and clean up files (#29)

Co-authored-by: Mikhail Mikhasenko <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

docs/HS3.md

@@ -20,3 +20,107 @@ In parallel to development of the model description format, compatibility with H
 - [HS3_extended.json](../models/HS3_extended.json) prototypes
   - adding jacobian (prior) for phase space generation,
   - replacing phase space variables
+
+## Parameters of the model
+
+The model parameters have to be listed in the parameter block of distributions.
+
+```jsonc
+"distributions": [
+  {
+    "name": "my_model_for_reaction_intensity",
+    "type": "hadronic_cross_section_unpolarized_dist",
+    "model_description": {
+    },
+    "variables": [
+    ],
+    "parameters": ["L_1520_mass"]
+  }
+]
+```
+
+The default values of the parameters are not mandatory, however, they can be listed as one of the element of the `parameter_points` array.
+
+```jsonc
+"parameter_points": [
+  {
+    "name": "default_values_of_my_model",
+    "parameters": [
+      {
+        "name": "L_1520_mass",
+        "value": 1.52
+      }
+    ]
+  }
+]
+```
+
+The validation block has to include
+
+```jsonc
+"parameter_points": [
+  {
+    "name": "validation_point",
+    "parameters": [
+      {
+        "name": "L_1520_mass",
+        "value": 4.6
+      },
+      {
+        "name": "L_1520_mass",
+        "value": 4.6
+      },
+      {}
+    ]
+  },
+  {}
+]
+```
+
+## Sampling from the model
+
+To sample from the model using the kinematic variables defined in `variable` section, a few sections has to be added.
+
+```jsonc
+"likelihoods": [
+  {
+    "name": "my_nll",
+    "pdfs": ["my_model_for_reaction_intensity"],
+    "datasets": []
+  }
+]
+```
+
+**Likelihood** section clarifies how the log likelihood is computed from the `pdfs` .
+
+```jsonc
+"analyses": [
+  {
+    "name": "my_ana",
+    "parameter_domain": "default",
+    "prior": "my_prior_dist"
+  }
+]
+```
+
+**Analyses** specifies how kinematic variables are distributed within the phase space, using priors (here, `"prior": "my_prior_dist"`) to influence their sampling distributions.
+
+The priors are given in the list of distributions.
+
+```jsonc
+"distibutions": [
+  {},
+  {
+    "name": "my_prior_dist",
+    "type": "product_dist",
+    "elements": ["m12_prior"]
+  },
+  {
+    "name": "m12_prior",
+    "type": "phase_space_density_1d",
+    "variable": "m_12"
+  }
+]
+```
+
+Here we define `my_prior_dist` as a product distribution, supposedly incorporating all non-trivial dimensions of the phase-space density (the mass dimensions).

docs/julia/Manifest.toml

@@ -75,9 +75,9 @@ version = "0.10.0"
 
 [[deps.Colors]]
 deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
-git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a"
+git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.12.10"
+version = "0.12.11"
 
 [[deps.Compat]]
 deps = ["TOML", "UUIDs"]
@@ -269,9 +269,9 @@ version = "0.21.0+0"
 
 [[deps.Glib_jll]]
 deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "359a1ba2e320790ddbe4ee8b4d54a305c0ea2aff"
+git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.80.0+0"
+version = "2.80.2+0"
 
 [[deps.GraphPlot]]
 deps = ["ArnoldiMethod", "ColorTypes", "Colors", "Compose", "DelimitedFiles", "Graphs", "LinearAlgebra", "Random", "SparseArrays"]
@@ -298,9 +298,9 @@ version = "1.0.2"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "ab5b37dc4f98fc037527968852a6f9b2bdf9f32d"
+git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.10.7"
+version = "1.10.8"
 
 [[deps.HadronicLineshapes]]
 deps = ["Parameters", "QuadGK", "StaticArrays"]
@@ -477,9 +477,9 @@ version = "1.17.0+0"
 
 [[deps.Libmount_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "4b683b19157282f50bfd5dcaa2efe5295814ea22"
+git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e"
 uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
-version = "2.40.0+0"
+version = "2.40.1+0"
 
 [[deps.Libtiff_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
@@ -489,9 +489,9 @@ version = "4.5.1+1"
 
 [[deps.Libuuid_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "27fd5cc10be85658cacfe11bb81bee216af13eda"
+git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807"
 uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
-version = "2.40.0+0"
+version = "2.40.1+0"
 
 [[deps.LinearAlgebra]]
 deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
@@ -659,9 +659,9 @@ version = "1.3.0"
 
 [[deps.Pixman_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"]
-git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87"
+git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b"
 uuid = "30392449-352a-5448-841d-b1acce4e97dc"
-version = "0.42.2+0"
+version = "0.43.4+0"
 
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
@@ -812,9 +812,9 @@ version = "1.2.1"
 
 [[deps.SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "0e7508ff27ba32f26cd459474ca2ede1bc10991f"
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 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
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+version = "1.4.2"
 
 [[deps.Serialization]]
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