PDS removal, Maintainer tools (#3)

- Remove all PDS tools, since archiving will take place in Astromat - Add maintainer tools to add new database releases to the `json` files that describe all db versions, etc. - Add documentation - Tests for maintainer tools - Upgrade license years
NASA-Planetary-Science · Aug 24, 2023 · e02bf5e · e02bf5e
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diff --git a/.github/workflows/rimseval_testing.yml b/.github/workflows/rimseval_testing.yml
@@ -28,7 +28,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install nox
-        pip install .[dev,db_maintainer]
+        pip install .[dev,maintainer]
     - name: Run nox
       run: nox --no-error-on-missing-interpreters
     - name: Generate coverage report

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2020 Reto Trappitsch
+Copyright (c) 2020 - 2023 Reto Trappitsch
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/database/README.md b/database/README.md
@@ -1,31 +1,63 @@
-# Database
+# Database and information
 
 This folder serves a database file with links to all Zenodo releases of the databases.
-The links are stored in the `db.json` file.
+These json files are read in by the `pgdtools` whenever the database is updated.
+
+## Database versions and change log
+
+The links and descriptions are stored in the `db.json` file.
 Each entry in the `db.json` file has the following structure:
 
 ```json
 {
-    "db_short_name": {
-      "name": "Name of the database",
-      "versions": ["link-to_version1.csv", "link-to_version2.csv", ...]
+    "Sample Database": {
+      "db_name": "Name of the database",
+      "versions": [
+        {
+          "Change": "Description of what has changed in this version compared to the old ones",
+          "Date": "Date of the database release in YYYY-MM-DD format",
+          "DOI": "DOI of the database release",
+          "Grains": "Number of grains in the database",
+          "Known issues": "Known issues with this version of the database",
+          "Released on": "Where this database has been released",
+          "URL": "URL of the csv database",
+        }
+      ]
     }
 }
 ```
 
+The outer layer gives a database name (see below), e.g., `"sic"`.
+The inner layer has first a `"db_name"`,
+giving the database name in a human-readable format, e.g., `"Silicon Carbide"`.
+The `"versions"` list contains all versions of the database,
+where each version has multiple entries as described in the example `json` file above.
+
 The following databases are currently available:
 
 - Presolar SiC grains (`"sic"`)
 
-This json file is read in by the `pgdtools` whenever the database is updated.
+## Techniques
+
+The `techniques.json` file contains a list of all techniques that are currently in the presolar grain database.
+Each entry has the following structure:
 
-## Zenodo links
+```json
+{
+  "technqiue_name": {
+    "institution": "Institution where the technique was used",
+    "techique": "Name of the technique",
+    "instrument": "Name of the instrument",
+    "reference": "Reference to the publication where the instrument was described"
+  }
+}
+```
 
-The following links point to the Zenodo releases of the databases:
+Note that the `"technique_name"` is simply the name of the technique as given in the Excel file.
 
-- [Silicon Carbide](https://zenodo.org/record/8187488)
+## References
 
-## Changelog
+There are two files with references:
 
-In order to obtain the changelog of the databse,
-please refer to `.xlsx` files on Zenodo.
+- `references.json` contains all references that are used in the database, identical to the Excel file.
+- `references.bib` contains all references in BibTeX format.
diff --git a/database/db.json b/database/db.json
@@ -1,13 +1,61 @@
 {
     "sic": {
-        "name": "Silicon Carbide",
+        "db_name": "Silicon Carbide",
         "versions": [
-            "https://zenodo.org/record/8187220/files/PGD_SiC_2019-12-20.csv",
-            "https://zenodo.org/record/8187406/files/PGD_SiC_2020-01-03.csv",
-            "https://zenodo.org/record/8187446/files/PGD_SiC_2020-08-18.csv",
-            "https://zenodo.org/record/8187471/files/PGD_SiC_2020-12-24.csv",
-            "https://zenodo.org/record/8187479/files/PGD_SiC_2021-01-10.csv",
-            "https://zenodo.org/record/8187488/files/PGD_SiC_2023-07-22.csv"
+            {
+                "Change": "New start of the Presolar Grain Database after a complete rebuild.\n",
+                "Date": "2019-12-20",
+                "DOI": "10.5281/zenodo.8187220",
+                "Grains": 16000,
+                "Known issues": "New grain type assignment still needs to be worked on. Much more data to add.\n",
+                "Released on": "Zenodo",
+                "URL": "https://zenodo.org/record/8187220/files/PGD_SiC_2019-12-20.csv"
+            },
+            {
+                "Change": "1. Data with delta values < -1000 removed.\n2. Some grain type assignments corrected.\n3. Some grain labels corrected according to nomenclature in respective publication.\n4. Missing techniques added.\n5. Sheet \"Techniques\" added.\n",
+                "Date": "2020-01-03",
+                "DOI": "10.5281/zenodo.8187406",
+                "Grains": 16000,
+                "Known issues": "New grain type assignment still needs to be worked on. Much more data to add.\n",
+                "Released on": "Zenodo",
+                "URL": "https://zenodo.org/record/8187406/files/PGD_SiC_2020-01-03.csv"
+            },
+            {
+                "Change": "1. Changed number format to show all digits.\n2. C and Si data (uncertainties) from Liu et al. (2014) ApJ 786:66 corrected. Reported as 2 sigma but are 1 sigma instead.\n3. Added new columns for strontium data normalized to 87Sr.\n4. Data from following references added:\nLiu et al. (2015) ApJ 803:12\nLiu et al. (2016) ApJ 820:140\nLiu et al. (2017) ApJL 842:L1\nLiu et al. (2017) ApJL 844:L12\nLiu et al. (2017) MAPS 12:2550\nHoppe et al. (2018) GCA 221:182\nLiu et al. (2018) SciA 4:eaao1054\nLiu et al. (2018) ApJ 855:144\nNguyen et al. (2018) GCA 221:162\nHoppe et al. (2019) ApJ 887:8\nLiu et al. (2019) ApJ 881:28\n",
+                "Date": "2020-08-18",
+                "DOI": "10.5281/zenodo.8187446",
+                "Grains": 19759,
+                "Known issues": "New grain type assignment still needs to be worked on. Much more data to add.\n",
+                "Released on": "Zenodo",
+                "URL": "https://zenodo.org/record/8187446/files/PGD_SiC_2020-08-18.csv"
+            },
+            {
+                "Change": "1. Corrected typo in reference (volume number 52 instead of 12) for SiC-2017-LIU-2 data.\n2. Grain type asignment for 10 Grains from Nguyen et al. (2018) GCA 221:162 Changed from M to AB.\n3. Data from the following references added:\nKodolányi et al. (2018) GCA 221:127\nTrappitsch et al. (2018) GCA 221:87\n",
+                "Date": "2020-12-24",
+                "DOI": "10.5281/zenodo.8187471",
+                "Grains": 19864,
+                "Known issues": "New grain type assignment still needs to be worked on. Much more data to add.\n",
+                "Released on": "Zenodo",
+                "URL": "https://zenodo.org/record/8187471/files/PGD_SiC_2020-12-24.csv"
+            },
+            {
+                "Change": "1. Grain type asignment Changed to AB for Grains M and Z Grains with 12C/13C < 12.3.\n2. Some minor adjustments in grain type assignments.\n3. Grain subtypes introduced.\n4. Data from the following references added:\nFloss & Stadermann (2009) ApJ 697:1242\nNguyen et al. (2010) ApJ 719:166\nLeitner et al. (2012) ApJ 745:38\nHaenecour et al. (2018) GCA 221:379\nNittler et al. (2018) GCA 226:107\n",
+                "Date": "2021-01-10",
+                "DOI": "10.5281/zenodo.8187479",
+                "Grains": 19976,
+                "Known issues": "New grain type and subtype asignments still need to be worked on, especially for separation between M, Y, and Z.\n",
+                "Released on": "Zenodo",
+                "URL": "https://zenodo.org/record/8187479/files/PGD_SiC_2021-01-10.csv"
+            },
+            {
+                "Change": "1. New PGD Type asignments including new Type D.\n2. Now probabilities for being consistent with a given grain type are provided.\n3. Size is now split up into Size a and Size b with only numerical entries.\n4. Zero uncertainties in err[12C/13C] replaced by best estimate.\n5. Some notes added.\n6. Corrected typo in abbreviated reference (Hoppe et al. (2019) ApJ 887:8).\n7. Data from the following references added:\nNIttler et al. (2020) MAPS 55:1160\nLiu et al. (2021) ApJL 920:L26\nNIttler et al. (2021) MAPS 56:260\nBarosch et al. (2022) ApJL 935:L3\nBarosch et al. (2022) GCA 335:169\nLiu et al. (2022) EPJA 58:216\nHoppe et al. (2023) ApJL 943:L22\n",
+                "Date": "2023-07-22",
+                "DOI": "10.5281/zenodo.8187488",
+                "Grains": 20230,
+                "Known issues": "",
+                "Released on": "Zenodo",
+                "URL": "https://zenodo.org/record/8187488/files/PGD_SiC_2023-07-22.csv"
+            }
         ]
     }
 }
diff --git a/pgdtools/data/pgd_references.bib → database/pgd_references.bib b/pgdtools/data/pgd_references.bib → database/pgd_references.bib
diff --git a/docs/db_maintainer/pds.rst b/docs/db_maintainer/pds.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -43,7 +43,8 @@ Contents
     :maxdepth: 2
     :caption: Database Maintainer
 
-    db_maintainer/pds
+    maintainer/overview
+    maintainer/db_addition
 
 .. toctree::
     :maxdepth: 2

diff --git a/docs/license.rst b/docs/license.rst
@@ -3,7 +3,7 @@ License
 
 MIT License
 
-Copyright (c) 2021-2022 Reto Trappitsch
+Copyright (c) 2021-2023 Reto Trappitsch
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal