v1.5.0 Prep (#721)

javh · bussec · web-flow · commit bac6e42f7b35 · 2023-08-28T09:30:47.000-07:00
* Update schema changelog.
* Updated changelog for R and python packages
* R package version bump
* Update germline example in R package.
* Rebuild R docs

---------

Co-authored-by: Christian Busse &lt;christian.busse@dkfz-heidelberg.de&gt;
diff --git a/docs/packages/airr-R/news.rst b/docs/packages/airr-R/news.rst
@@ -1,6 +1,11 @@
 Release Notes
 =============
 
+Version 1.5.0: August 28, 2023
+------------------------------
+
+-  Updated schema set and examples to v1.5.
+
 Version 1.4.1: August 27, 2022
 ------------------------------
 
diff --git a/docs/packages/airr-R/overview.rst b/docs/packages/airr-R/overview.rst
@@ -1,6 +1,6 @@
 .. _ROverview:
 
-R Library
+AIRR R Reference Library
 =================================================================================
 
 ``airr`` is an R package for working with data formatted according to
diff --git a/docs/packages/airr-R/topics/read_tabular.rst b/docs/packages/airr-R/topics/read_tabular.rst
@@ -69,6 +69,7 @@ Examples
 
    # Load data file
    df <- read_rearrangement(file)
+                                                                                                                                                                                   
 
 See also
 ~~~~~~~~
diff --git a/docs/packages/airr-R/topics/validate_tabular.rst b/docs/packages/airr-R/topics/validate_tabular.rst
@@ -51,7 +51,6 @@ Examples
    # Load data file
    df <- read_rearrangement(file)
 
-
 .. code:: r
 
 
diff --git a/docs/packages/airr-R/topics/write_tabular.rst b/docs/packages/airr-R/topics/write_tabular.rst
@@ -62,15 +62,15 @@ Examples
 
    # Load data file
    df <- read_rearrangement(file)
-
+                                                                                                                                                                            
 
 .. code:: r
 
 
    # Write a Rearrangement data file
    outfile <- file.path(tempdir(), "output.tsv")
    write_tabular(df, outfile, schema=RearrangementSchema)
-
+                                                                                                                    
 
 See also
 ~~~~~~~~
diff --git a/docs/packages/airr-R/vignettes/Usage-Vignette.rst b/docs/packages/airr-R/vignettes/Usage-Vignette.rst
@@ -50,7 +50,7 @@ usage is straightforward, as the file format is a typical tabulated
 file. The argument that needs attention is ``base``, with possible
 values ``"0"`` and ``"1"``. ``base`` denotes the starting index for
 positional fields in the input file. Positional fields are those that
-contain alignment coordinates and names ending in "_start" and "_end".
+contain alignment coordinates and names ending in “\_start” and “\_end”.
 If the input file is using 1-based closed intervals (R style), as
 defined by the standard, then positional fields will not be modified
 under the default setting of ``base="1"``. If the input file is using
@@ -76,39 +76,39 @@ Reading Rearrangements
 
    ## Rows: 101
    ## Columns: 33
-   ## $ sequence_id        <chr> "SRR765688.7787", "SRR765688.35420", "SRR765688.36681", "SRR765688.33811", "SRR765688.44149", "SRR765688.15636", "SRR765688.20304", "SRR765688.13860", "SRR7656…
-   ## $ sequence           <chr> "NNNNNNNNNNNNNNNNNNNNGCTGACCTGCACCTTCTCTGGATTCTCACTCAGTACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGCCAAATATTACAGCACCAGCCC…
-   ## $ rev_comp           <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…
-   ## $ productive         <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE…
-   ## $ vj_in_frame        <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, T…
-   ## $ stop_codon         <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FAL…
-   ## $ v_call             <chr> "IGHV2-5*02", "IGHV5-51*01", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV2-5*02", "IGHV7-4-1*02", "IGHV6-1*01,IGHV6-1*02", "IGHV7-4-1*02", "IGHV4-39*0…
-   ## $ d_call             <chr> "IGHD5-24*01", "IGHD3-16*02,IGHD3-3*01,IGHD3-3*02", "IGHD3-22*01", "IGHD3-9*01", "IGHD1-26*01", "IGHD2-21*02", "IGHD1-26*01,IGHD2-21*02,IGHD3/OR15-3a*01", "IGH…
-   ## $ j_call             <chr> "IGHJ4*02", "IGHJ6*02,IGHJ6*04", "IGHJ4*02", "IGHJ6*02", "IGHJ6*01", "IGHJ4*02", "IGHJ5*02", "IGHJ4*02", "IGHJ4*02", "IGHJ4*02", "IGHJ5*02", "IGHJ6*02", "IGHJ6…
-   ## $ c_call             <chr> "IGHG", "IGHG", "IGHG", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHG", "IGHA", "IGHG", "IGHG",…
-   ## $ sequence_alignment <chr> "...........................................................GCTGACCTGCACCTTCTCTGGATTCTCACTCAGT......ACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCT…
-   ## $ germline_alignment <chr> "CAGATCACCTTGAAGGAGTCTGGTCCT...ACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGC......ACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCT…
-   ## $ junction           <chr> "TGTGCACACAGTGCGGGATGGCTGCCTGATTACTGG", "TGTGCGAGGCATGGATTATACGGTTGTGATCATACCGGCTGTTATACAAGCTTCTACTACTACGGGATGGACGTCTGG", "TGTGCGAGAGAAGAACGTCGAAGTAGTGGTTATTTT…
-   ## $ junction_aa        <chr> "CAHSAGWLPDYW", "CARHGLYGCDHTGCYTSFYYYGMDVW", "CAREERRSSGYFDHW", "CAREGYYFDTTGSPRSHGLDVW", "CARDSGGMDVW", "CVLSRRLGDSGVQKYYFDYW", "CAREGLWDGRVVTDLW", "CARTRYSS…
-   ## $ v_cigar            <chr> "20S56N21=1X11=1X7=1X9=3X62=6D2=1X1=2X2=2X50=1X7=1X4=1X22=1X30=", "20S40N15=1X15=1X11=1X2=1X1=1X1=2X3=1X7=1X41=2X2=1X10=1X3=1X1=1X5=2X5=1X4=1X9=1X19=1X24=2X9=1…
-   ## $ d_cigar            <chr> "274S5N7=", "305S29N7=", "293S13N12=", "290S9N8=", "283S4N7=", "273S12N8=", "289S6N6=", "267S9N9=", "281S7N5=", "278S7N5=1X7=", "277S8N7=", "297S9N7=", "265S9N…
-   ## $ j_cigar            <chr> "288S11N32=1X4=", "318S7N12=1X15=", "305S5N6=1X14=1X21=", "321S15N5=1X23=1X17=", "290S17N19=", "296S26=1X21=", "311S11N4=1X33=", "280S2N17=1X6=1X21=", "299S8N4…
-   ## $ v_sequence_start   <int> 21, 21, 21, 21, 21, 21, 21, 20, 22, 21, 21, 20, 21, 21, 21, 21, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 20, 23, 19, 21, 20, 21, 21, 20, 20, 21, 20, 22, 21, 21,…
-   ## $ v_sequence_end     <int> 269, 276, 283, 283, 283, 264, 283, 259, 281, 266, 264, 294, 258, 283, 273, 279, 274, 259, 278, 280, 262, 271, 281, 262, 264, 283, 259, 279, 278, 280, 261, 260,…
-   ## $ v_germline_start   <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
-   ## $ v_germline_end     <int> 320, 320, 320, 320, 320, 320, 320, 318, 318, 320, 320, 320, 319, 319, 317, 316, 316, 320, 318, 320, 320, 315, 318, 320, 321, 320, 318, 316, 320, 317, 319, 316,…
-   ## $ d_sequence_start   <int> 275, 306, 294, 291, 284, 274, 290, 268, 282, 279, 278, 298, 266, 292, 301, 285, 276, NA, 291, 284, 273, 279, 289, 277, 272, 299, 270, 292, 282, 295, 267, 265, …
-   ## $ d_sequence_end     <int> 281, 312, 305, 298, 290, 281, 295, 276, 286, 291, 284, 304, 273, 296, 307, 289, 282, NA, 297, 295, 293, 290, 294, 283, 287, 307, 280, 302, 290, 301, 280, 270, …
-   ## $ d_germline_start   <int> 6, 30, 14, 10, 5, 13, 7, 10, 8, 8, 9, 10, 10, 7, 22, 14, 4, NA, 24, 4, 2, 5, 8, 9, 6, 3, 1, 3, 7, 7, 4, 6, 11, 14, 12, 8, 2, 11, 8, 10, 5, 24, 4, 17, 5, 5, 4, …
-   ## $ d_germline_end     <int> 12, 36, 25, 17, 11, 20, 12, 18, 12, 20, 15, 16, 17, 11, 28, 18, 10, NA, 30, 15, 22, 16, 13, 15, 21, 11, 11, 13, 15, 13, 17, 11, 17, 18, 19, 13, 8, 16, 20, 16, …
-   ## $ j_sequence_start   <int> 289, 319, 306, 322, 291, 297, 312, 281, 300, 301, 289, 319, 276, 300, 317, 299, 296, 271, 336, 321, 303, 304, 300, 297, 293, 322, 289, 311, 315, 320, 283, 293,…
-   ## $ j_sequence_end     <int> 325, 346, 348, 368, 309, 344, 349, 326, 339, 347, 335, 361, 326, 334, 350, 333, 346, 320, 370, 338, 332, 338, 339, 333, 340, 368, 332, 345, 342, 362, 327, 327,…
-   ## $ j_germline_start   <int> 12, 8, 6, 16, 18, 1, 12, 3, 9, 2, 5, 20, 9, 14, 15, 14, 2, 13, 28, 18, 6, 14, 9, 15, 1, 16, 5, 14, 8, 5, 4, 12, 9, 1, 20, 15, 6, 6, 5, 6, 5, 9, 1, 6, 5, 5, 9, …
-   ## $ j_germline_end     <int> 48, 35, 48, 62, 36, 48, 49, 48, 48, 48, 51, 62, 59, 48, 48, 48, 52, 62, 62, 35, 35, 48, 48, 51, 48, 62, 48, 48, 35, 47, 48, 46, 48, 44, 62, 48, 48, 51, 50, 53,…
-   ## $ junction_length    <int> 36, 78, 45, 66, 33, 60, 48, 45, 36, 61, 51, 48, 51, 30, 54, 30, 48, 42, 71, 66, 78, 42, 36, 51, 57, 66, 51, 42, 72, 60, 45, 45, 45, 42, 36, 36, 57, 48, 51, 45,…
-   ## $ np1_length         <int> 5, 29, 10, 7, 0, 9, 6, 8, 0, 12, 13, 3, 7, 8, 27, 5, 1, 11, 12, 3, 10, 7, 7, 14, 7, 15, 10, 12, 3, 14, 5, 4, 4, 6, 1, 7, 1, 5, 4, 5, 26, 5, 0, 15, 26, 26, 8, 7…
-   ## $ np2_length         <int> 7, 6, 0, 23, 0, 15, 16, 4, 13, 9, 4, 14, 2, 3, 9, 9, 13, NA, 38, 25, 9, 13, 5, 13, 5, 14, 8, 8, 24, 18, 2, 22, 15, 3, 3, 11, 29, 11, 9, 5, 1, 5, 8, 0, 1, 1, 11…
-   ## $ duplicate_count    <int> 3, 3, 13, 3, 2, 2, 4, 2, 2, 2, 4, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 5, 2, 2, 3, 2, 4, 2, 3, 4, 8, 2, 2, 2, 2, 3, 2, 4, 3, 4, 2, 5, 2, 2, 7, 3, 2,…
+   ## $ sequence_id        <chr> "SRR765688.7787", "SRR765688.35420", "SRR765688.36681", "SRR765688.33811", "SRR765688.44149", "SRR765688.15636", "SRR765688.20304", "SRR765688.13860", "SRR7…
+   ## $ sequence           <chr> "NNNNNNNNNNNNNNNNNNNNGCTGACCTGCACCTTCTCTGGATTCTCACTCAGTACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGCCAAATATTACAGCACCAG…
+   ## $ rev_comp           <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA…
+   ## $ productive         <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, T…
+   ## $ vj_in_frame        <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE…
+   ## $ stop_codon         <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, …
+   ## $ v_call             <chr> "IGHV2-5*02", "IGHV5-51*01", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV2-5*02", "IGHV7-4-1*02", "IGHV6-1*01,IGHV6-1*02", "IGHV7-4-1*02", "IGHV4-3…
+   ## $ d_call             <chr> "IGHD5-24*01", "IGHD3-16*02,IGHD3-3*01,IGHD3-3*02", "IGHD3-22*01", "IGHD3-9*01", "IGHD1-26*01", "IGHD2-21*02", "IGHD1-26*01,IGHD2-21*02,IGHD3/OR15-3a*01", "…
+   ## $ j_call             <chr> "IGHJ4*02", "IGHJ6*02,IGHJ6*04", "IGHJ4*02", "IGHJ6*02", "IGHJ6*01", "IGHJ4*02", "IGHJ5*02", "IGHJ4*02", "IGHJ4*02", "IGHJ4*02", "IGHJ5*02", "IGHJ6*02", "IG…
+   ## $ c_call             <chr> "IGHG", "IGHG", "IGHG", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHG", "IGHA", "IGHG", "IGH…
+   ## $ sequence_alignment <chr> "...........................................................GCTGACCTGCACCTTCTCTGGATTCTCACTCAGT......ACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTG…
+   ## $ germline_alignment <chr> "CAGATCACCTTGAAGGAGTCTGGTCCT...ACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGC......ACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTG…
+   ## $ junction           <chr> "TGTGCACACAGTGCGGGATGGCTGCCTGATTACTGG", "TGTGCGAGGCATGGATTATACGGTTGTGATCATACCGGCTGTTATACAAGCTTCTACTACTACGGGATGGACGTCTGG", "TGTGCGAGAGAAGAACGTCGAAGTAGTGGTTAT…
+   ## $ junction_aa        <chr> "CAHSAGWLPDYW", "CARHGLYGCDHTGCYTSFYYYGMDVW", "CAREERRSSGYFDHW", "CAREGYYFDTTGSPRSHGLDVW", "CARDSGGMDVW", "CVLSRRLGDSGVQKYYFDYW", "CAREGLWDGRVVTDLW", "CARTR…
+   ## $ v_cigar            <chr> "20S56N21=1X11=1X7=1X9=3X62=6D2=1X1=2X2=2X50=1X7=1X4=1X22=1X30=", "20S40N15=1X15=1X11=1X2=1X1=1X1=2X3=1X7=1X41=2X2=1X10=1X3=1X1=1X5=2X5=1X4=1X9=1X19=1X24=2X…
+   ## $ d_cigar            <chr> "274S5N7=", "305S29N7=", "293S13N12=", "290S9N8=", "283S4N7=", "273S12N8=", "289S6N6=", "267S9N9=", "281S7N5=", "278S7N5=1X7=", "277S8N7=", "297S9N7=", "265…
+   ## $ j_cigar            <chr> "288S11N32=1X4=", "318S7N12=1X15=", "305S5N6=1X14=1X21=", "321S15N5=1X23=1X17=", "290S17N19=", "296S26=1X21=", "311S11N4=1X33=", "280S2N17=1X6=1X21=", "299S…
+   ## $ v_sequence_start   <int> 21, 21, 21, 21, 21, 21, 21, 20, 22, 21, 21, 20, 21, 21, 21, 21, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 20, 23, 19, 21, 20, 21, 21, 20, 20, 21, 20, 22, 21, …
+   ## $ v_sequence_end     <int> 269, 276, 283, 283, 283, 264, 283, 259, 281, 266, 264, 294, 258, 283, 273, 279, 274, 259, 278, 280, 262, 271, 281, 262, 264, 283, 259, 279, 278, 280, 261, 2…
+   ## $ v_germline_start   <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
+   ## $ v_germline_end     <int> 320, 320, 320, 320, 320, 320, 320, 318, 318, 320, 320, 320, 319, 319, 317, 316, 316, 320, 318, 320, 320, 315, 318, 320, 321, 320, 318, 316, 320, 317, 319, 3…
+   ## $ d_sequence_start   <int> 275, 306, 294, 291, 284, 274, 290, 268, 282, 279, 278, 298, 266, 292, 301, 285, 276, NA, 291, 284, 273, 279, 289, 277, 272, 299, 270, 292, 282, 295, 267, 26…
+   ## $ d_sequence_end     <int> 281, 312, 305, 298, 290, 281, 295, 276, 286, 291, 284, 304, 273, 296, 307, 289, 282, NA, 297, 295, 293, 290, 294, 283, 287, 307, 280, 302, 290, 301, 280, 27…
+   ## $ d_germline_start   <int> 6, 30, 14, 10, 5, 13, 7, 10, 8, 8, 9, 10, 10, 7, 22, 14, 4, NA, 24, 4, 2, 5, 8, 9, 6, 3, 1, 3, 7, 7, 4, 6, 11, 14, 12, 8, 2, 11, 8, 10, 5, 24, 4, 17, 5, 5, …
+   ## $ d_germline_end     <int> 12, 36, 25, 17, 11, 20, 12, 18, 12, 20, 15, 16, 17, 11, 28, 18, 10, NA, 30, 15, 22, 16, 13, 15, 21, 11, 11, 13, 15, 13, 17, 11, 17, 18, 19, 13, 8, 16, 20, 1…
+   ## $ j_sequence_start   <int> 289, 319, 306, 322, 291, 297, 312, 281, 300, 301, 289, 319, 276, 300, 317, 299, 296, 271, 336, 321, 303, 304, 300, 297, 293, 322, 289, 311, 315, 320, 283, 2…
+   ## $ j_sequence_end     <int> 325, 346, 348, 368, 309, 344, 349, 326, 339, 347, 335, 361, 326, 334, 350, 333, 346, 320, 370, 338, 332, 338, 339, 333, 340, 368, 332, 345, 342, 362, 327, 3…
+   ## $ j_germline_start   <int> 12, 8, 6, 16, 18, 1, 12, 3, 9, 2, 5, 20, 9, 14, 15, 14, 2, 13, 28, 18, 6, 14, 9, 15, 1, 16, 5, 14, 8, 5, 4, 12, 9, 1, 20, 15, 6, 6, 5, 6, 5, 9, 1, 6, 5, 5, …
+   ## $ j_germline_end     <int> 48, 35, 48, 62, 36, 48, 49, 48, 48, 48, 51, 62, 59, 48, 48, 48, 52, 62, 62, 35, 35, 48, 48, 51, 48, 62, 48, 48, 35, 47, 48, 46, 48, 44, 62, 48, 48, 51, 50, …
+   ## $ junction_length    <int> 36, 78, 45, 66, 33, 60, 48, 45, 36, 61, 51, 48, 51, 30, 54, 30, 48, 42, 71, 66, 78, 42, 36, 51, 57, 66, 51, 42, 72, 60, 45, 45, 45, 42, 36, 36, 57, 48, 51, …
+   ## $ np1_length         <int> 5, 29, 10, 7, 0, 9, 6, 8, 0, 12, 13, 3, 7, 8, 27, 5, 1, 11, 12, 3, 10, 7, 7, 14, 7, 15, 10, 12, 3, 14, 5, 4, 4, 6, 1, 7, 1, 5, 4, 5, 26, 5, 0, 15, 26, 26, 8…
+   ## $ np2_length         <int> 7, 6, 0, 23, 0, 15, 16, 4, 13, 9, 4, 14, 2, 3, 9, 9, 13, NA, 38, 25, 9, 13, 5, 13, 5, 14, 8, 8, 24, 18, 2, 22, 15, 3, 3, 11, 29, 11, 9, 5, 1, 5, 8, 0, 1, 1,…
+   ## $ duplicate_count    <int> 3, 3, 13, 3, 2, 2, 4, 2, 2, 2, 4, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 5, 2, 2, 3, 2, 4, 2, 3, 4, 8, 2, 2, 2, 2, 3, 2, 4, 3, 4, 2, 5, 2, 2, 7, 3,…
 
 Reading AIRR Data Models
 ~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/docs/standards/news.rst b/docs/standards/news.rst
@@ -3,12 +3,67 @@
 Schema Release Notes
 ================================================================================
 
-Version 1.4.2: TBD, 2023
+Version 1.5.0: August 31, 2023
 --------------------------------------------------------------------------------
 
-1. Added "IGI" to all locus enum fields.
+**Version 1.5 schema release.**
+
+General Schema Changes:
+
+1. Fixed synchronization errors between the OpenAPI v2 and v3 versions of the
+   AIRR Schema (airr-schema.yaml and airr-schema-openapi3.yaml).
+2. Set the default value of ``x-airr.miarr`` attributes to ``defined``.
+3. Converted all ``x-airr.format`` attribute values to snake_case, which
+   specifically impacts any instance of ``controlled vocabulary`` or
+   ``physical quantity``.
+4. Corrected numerous instances of missing `x-airr.miairr` and
+   `x-airr.identifier` attributes.
+5. Replaced ``x-airr.adc-api-optional`` attribute with
+   ``x-airr.adc-query-support`` in multiple fields.
+6. Added "IGI" as a valid value to the ``locus`` enum fields in multiple
+   schema.
+7. Added ``null`` as a valide value to all nullable enum fields.
+8. Removed ``discriminator: AIRR`` from all object definitions.
+
+Germline and Genotype Schema:
+
+1. Clarified the descriptions of multiple fields in the Germline and
+   Genotype schema.
 2. Modified ``x-airr: nullable`` and ``x-airr: identifier`` values on multiple
-   Germline schema.
+   fields in the Germline and Genotype schema.
+3. Removed the ``alignment`` field and added the ``unaligned_sequence``,
+   ``aligned_sequences``, and ``alignment_labels`` fields to the
+   ``SequenceDelineationV`` object.
+4. Converted the enum values in the ``inference_type`` field of
+   ``AlleleDescription`` to snake_case.
+5. Added the ``allele_similarity_cluster_designation`` and
+   ``allele_similarity_cluster_member_id`` fields to ``AlleleDescription``.
+6. Moved the nested objects ``DocumentedAllele``, ``UndocumentedAllele``, and
+   ``DeletedGenes`` out of ``Genotype`` and defined them as top-level objects
+   references by the ``documented_alleles``, ``undocumented_alleles``, and
+   ``deleted_genes`` fields, respectively.
+7. Moved the nested object ``MHCAllele`` out of ``MHCGenotype`` and defined
+   it as a top-level object referenced by the ``mhc_alleles`` field.
+
+Single-cell Schema:
+
+1. Added the ``property_type`` field to the ``CellExpression`` object.
+2. Moved the nested ``ReceptorReactivity`` object out of ``Receptor``
+   and defined it as a top-level object referenced by the
+   ``reactivity_measurements`` field.
+
+Subject Schema:
+
+1. Removed the nested references to ``GenotypeSet`` and ``MHCGenotypeSet``
+   in the ``genotype`` field and modified the definition to point to a
+   top-level ``SubjectGenotype`` object defining these references.
+
+DataProcessing Schema:
+
+1. Clarified the description of ``quality_thresholds`` to indicate that
+   quality filtering is not mandatory.
+
+
 
 Version 1.4.1: August 27, 2022
 --------------------------------------------------------------------------------
diff --git a/lang/R/DESCRIPTION b/lang/R/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: airr
 Type: Package
-Version: 1.4.1
-Date: 2022-08-27
+Version: 1.5.0
+Date: 2023-08-28
 Authors@R: c(person("Jason", "Vander Heiden", role=c("aut", "cre"), 
                     email="jason.vanderheiden@gmail.com"),
              person("Susanna", "Marquez", role=c("aut"), 
@@ -39,4 +39,4 @@ Suggests:
     rmarkdown,
     tibble,
     testthat
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
diff --git a/lang/R/NEWS.md b/lang/R/NEWS.md
@@ -1,3 +1,9 @@
+Version 1.5.0:  August 28, 2023
+-------------------------------------------------------------------------------
+ 
++ Updated schema set and examples to v1.5.
+
+
 Version 1.4.1:  August 27, 2022
 -------------------------------------------------------------------------------
 
diff --git a/lang/R/docs/build.R b/lang/R/docs/build.R
@@ -6,5 +6,5 @@ build_mkdocs(".", doc_path=doc_path, style="sphinx", yaml=F)
 run_pandoc(doc_path, format="rst", delete=T)
 
 # TODO: Post execution we still need to do cleanup:
-# Edit the title and about in docs/packages/airr-R/overview.rst
+# Edit the title and about in docs/packages/airr-R/overview.rst and about.rst
 # Remove the progress bar from the example in docs/*_tabular.rst and docs/ExampleData.rst
diff --git a/lang/R/inst/extdata/germline-example.json b/lang/R/inst/extdata/germline-example.json
diff --git a/lang/python/NEWS.rst b/lang/python/NEWS.rst
