Merge pull request #431 from pepkit/dev_tab_completion

tab completion

bash_complete.sh

@@ -0,0 +1,17 @@
+# Begin looper bash autocomplete
+_looper_autocomplete()
+{
+    local cur prev opts1
+    cur=${COMP_WORDS[COMP_CWORD]}
+    prev=${COMP_WORDS[COMP_CWORD-1]}
+    opts1=$(looper --commands)
+    case ${COMP_CWORD} in
+        1)
+            COMPREPLY=($(compgen -W "${opts1}" -- ${cur}))
+            ;;
+        2)
+            COMPREPLY=()
+            ;;
+    esac
+} && complete -o bashdefault -o default -F _looper_autocomplete looper
+# end looper bash autocomplete

docs/advanced.md

@@ -56,3 +56,30 @@ Once a pipeline is submitted any remaining interface files will be ignored.
 Until an appropriate pipeline is found, each interface file will be considered in succession.
 If no suitable pipeline is found in any interface, the sample will be skipped.
 In other words, the `pipeline_interfaces` value specifies a *prioritized* search list.
+
+## Set up tab completion
+
+Source `bash_complete.sh` to your `~/.bashrc` to get basic tab completion for Looper.
+
+Then, simply type `looper <tab> <tab>` to see a list of commands and `looper comma<tab>` to get autocompletion for specific commands.
+
+Source script to add to `~/.bashrc`:
+```bash
+# Begin looper bash autocomplete
+_looper_autocomplete()
+{
+    local cur prev opts1
+    cur=${COMP_WORDS[COMP_CWORD]}
+    prev=${COMP_WORDS[COMP_CWORD-1]}
+    opts1=$(looper --commands)
+    case ${COMP_CWORD} in
+        1)
+            COMPREPLY=($(compgen -W "${opts1}" -- ${cur}))
+            ;;
+        2)
+            COMPREPLY=()
+            ;;
+    esac
+} && complete -o bashdefault -o default -F _looper_autocomplete looper
+# end looper bash autocomplete
+```

docs/changelog.md

@@ -6,13 +6,17 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Added
 - `looper link` creates symlinks for results grouped by record_identifier. It requires pipestat to be configured. [#72](https://github.com/pepkit/looper/issues/72)
+- basic tab completion 
 
 ### Changed
 - looper now works with pipestat v0.6.0 and greater.
 - `looper table`, `check` now use pipestat and therefore require pipestat configuration. [#390](https://github.com/pepkit/looper/issues/390)
 - changed how looper configures pipestat [#411](https://github.com/pepkit/looper/issues/411)
 - initializing pipeline interface also writes an example `output_schema.yaml` and `count_lines.sh` pipeline
 
+### Fixed
+- filtering via attributes that are integers.
+
 ## [1.5.1] -- 2023-08-14
 
 ### Fixed

looper/cli_looper.py

@@ -495,6 +495,12 @@ def add_subparser(cmd):
             help="Number of attributes to display",
             type=int,
         )
+        parser.add_argument(
+            "--commands",
+            action="version",
+            version="{}".format(" ".join(subparsers.choices.keys())),
+        )
+
         result.append(parser)
     return result