add limited handling of deprecated cli options

Also fixed example for --jre-option in documentation. Was misnamed and
requires a value.

CHANGES.md

@@ -4,6 +4,8 @@
 
 ### Fixed
   - Updated shebangs to 'python3'. Patch courtesy of Andreas Tille.
+  - Added minimal support for previously removed command-line options, to prevent the
+    pipelines from failing when used with old configuration files.
 
 
 ## [1.3.0] - 2020-08-31

docs/bam_pipeline/configuration.rst

@@ -14,7 +14,7 @@ This is accomplished by writing options in `~/.paleomix/bam_pipeline.ini`::
     jar-root = /home/username/install/jar_root
     bwa-max-threads = 1
     temp-root = /tmp/username/bam_pipeline
-    jre-options =
+    jre-option = -Xmx4g
     bowtie2-max-threads = 1
 
 Options in the configuration file correspond directly to command-line options for the BAM pipeline, with leading dashes removed. For example, the command-line option `--max-threads` becomes `max-threads` in the configuration file.

paleomix/pipelines/bam/config.py

@@ -27,7 +27,7 @@
 import paleomix.common.logging
 
 from paleomix.resources import add_copy_example_command
-from paleomix.common.argparse import ArgumentParser
+from paleomix.common.argparse import ArgumentParser, SUPPRESS
 
 
 _DEFAULT_CONFIG_FILES = [
@@ -176,3 +176,8 @@ def add_run_command(subparsers):
         "to the JRE (Jave Runtime Environment); e.g. to change the "
         "maximum amount of memory (default is -Xmx4g)",
     )
+
+    # Removed options
+    parser.add_argument("--gatk-max-threads", help=SUPPRESS)
+    parser.add_argument("--progress-ui", help=SUPPRESS)
+    parser.add_argument("--ui-colors", help=SUPPRESS)

paleomix/pipelines/phylo/config.py

@@ -97,7 +97,6 @@ def build_parser():
         default="./data/prefixes",
         help="Location of prefixes (FASTAs) [%(default)s]",
     )
-    group.add_argument("--refseq-root", help=SUPPRESS)
     group.add_argument(
         "--destination",
         default="./results",
@@ -127,4 +126,9 @@ def build_parser():
         "with version requirements (if any).",
     )
 
+    # Removed options
+    parser.add_argument("--refseq-root", help=SUPPRESS)
+    parser.add_argument("--progress-ui", help=SUPPRESS)
+    parser.add_argument("--ui-colors", help=SUPPRESS)
+
     return parser

paleomix/pipelines/zonkey/config.py

@@ -190,4 +190,8 @@ def add_run_command(subparsers):
         "with version requirements (if any).",
     )
 
+    # Removed options
+    parser.add_argument("--progress-ui", help=SUPPRESS)
+    parser.add_argument("--ui-colors", help=SUPPRESS)
+
     return parser