Changing CSV argument to --csv or -o

.devcontainer/devcontainer.json

@@ -12,7 +12,7 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt",
+	"postCreateCommand": "pip3 install --user -r requirements.txt && pip install -e .",
 	"customizations": {
 		"vscode": {
 			"extensions": [

.gitignore

@@ -212,3 +212,4 @@ pyrightconfig.json
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
+out.csv

Jenkinsfile

@@ -32,22 +32,27 @@ pipeline {
         stage("publish") {
             parallel {
                 stage ("git.reslate.systems") {
+                    when {
+                        not {
+                            tag '*.*.*'
+                        }
+                    }
                     environment {
-                        TOKEN = credentials('git.reslate.systems')
+                        CREDS = credentials('username-password-rs-git')
                     }
                     steps {
-                        sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
                 stage ("pypi.org") {
                     when {
-                        tag '*.*'
+                        tag '*.*.*'
                     }
                     environment {
                         TOKEN = credentials('pypi.org')
                     }
                     steps {
-                        sh returnStatus: true, script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
             }

README.md

@@ -12,6 +12,7 @@ This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/a
 - Fetch the available BIGSdb database schemas for a given MLST database
 - Retrieve exact/non-exact MLST allele variant IDs based off a sequence
 - Retrieve MLST sequence type IDs based off a sequence
+- Inexact matches are annotated with an asterisk (\*)
 - Output all results to a single CSV
 
 ## Planned Features for CLI
@@ -40,6 +41,18 @@ Let's say you have a fasta called `seq.fasta` which contains several sequences.
 
 3. Then, run `autobigs st -h` and familiarize yourself with the parameters needed for sequence typing.
 
-4. Namely, you should find that you will need to run `autobigs st seq.fasta pubmlst_bordetella_seqdef 3 output.csv`. You can optionally include multiple `FASTA` files, and/or `--exact` to only retrieve exact sequence types, and/or `--stop-on-fail` to stop typing if one of your sequences fail to retrieve any type. 
+4. Namely, you should find that you will need to run `autobigs st seq.fasta pubmlst_bordetella_seqdef 3 output.csv`. You can optionally include multiple `FASTA` files, and `--stop-on-fail` to stop typing if one of your sequences fail to retrieve any type. 
 
-5. Sit tight, and wait. The `output.csv` will contain your results once completed.
+5. Sit tight, and wait. The `output.csv` will contain your results once completed.
+
+## Versioning
+
+the autoBIGS project follows [semantic versioning](https://semver.org/) where the three numbers may be interpreted as MAJOR.MINOR.PATCH.
+
+Note regarding major version 0 ([spec item 4](https://semver.org/#spec-item-4)), the following adaptation of semantic versioning definition is as follows:
+
+1. Given x.Y.z, Y is only incremented when a backwards incompatible change is made.
+
+2. Given x.y.Z, Z is only incremented when a backwards compatible change is made.
+
+Versions of autoBIGS items with a major version number of 0 will introduce numerous changes and patches. As such, changes between such versions should be considered highly variable.

pyproject.toml

@@ -6,16 +6,16 @@ build-backend = "setuptools.build_meta"
 name = "autoBIGS.cli"
 dynamic = ["version"]
 readme = "README.md"
-license = {file = "LICENSE"}
+license = {text = "GPL-3.0-or-later"}
 dependencies = [
-    "autoBIGS-engine"
+    "autoBIGS-engine==0.12.*"
 ]
 requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
 [project.urls]
-Repository = "https://github.com/RealYHD/autoBIGS.cli"
-Issues = "https://github.com/RealYHD/autoBIGS.cli/issues"
+Repository = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli"
+Issues = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli/issues"
 
 
 [project.scripts]

src/autobigs/cli/info.py

@@ -1,6 +1,8 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
-from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
+import csv
+from os import path
+from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
     parser.description = "Fetches the latest BIGSdb MLST database definitions."
@@ -24,22 +26,50 @@ def setup_parser(parser: ArgumentParser):
         help="Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given."
     )
 
+    parser.add_argument(
+        "--csv", "-o",
+        dest="csv_output",
+        required=False,
+        default=None,
+        help="Output list as CSV at a given path. A suffix is added depending on the action taken."
+    )
+
     parser.set_defaults(run=run_asynchronously)
     return parser
 
 async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
+        if args.list_dbs and len(args.list_bigsdb_schemas) > 0:
+            print("Cannot specify both database listing and schema listing, please choose one!")
+            exit(1)
+
         if args.list_dbs:
             known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
-            print("\n".join(known_seqdef_dbs.keys()))
+            sorted_seqdef_dbs = [(name, source) for name, source in sorted(known_seqdef_dbs.items())]
+            print("The following are all known BIGS database names, and their source (sorted alphabetically):")
+            print("\n".join(["{0}: {1}".format(name, source) for name, source in sorted_seqdef_dbs]))
+            if args.csv_output:
+                with open(args.csv_output, "w") as csv_out_handle:
+                    writer = csv.writer(csv_out_handle)
+                    writer.writerow(("BIGSdb Names", "Source"))
+                    writer.writerows(sorted_seqdef_dbs)
+                    print("\nDatabase output written to {0}".format(args.csv_output))
 
         for bigsdb_schema_name in args.list_bigsdb_schemas:
             schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
-            for schema_desc, schema_id in schemas.items():
-                print(f"{schema_desc}: {schema_id}")
+            sorted_schemas = [(name, id) for name, id in sorted(schemas.items())]
+            print("The following are the known schemas for \"{0}\", and their associated IDs:".format(bigsdb_schema_name))
+            print("\n".join(["{0}: {1}".format(name, id) for name, id in sorted_schemas]))
+            if args.csv_output:
+                with open(args.csv_output, "w") as csv_out_handle:
+                    writer = csv.writer(csv_out_handle)
+                    writer.writerow(("Name", "ID"))
+                    writer.writerows(sorted_schemas)
+                    print("\nSchema list output written to {0}".format(args.csv_output))
 
         if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
-            print("Nothing to do. Try specifying \"-l\".")
+            print("Nothing to do. Try specifying \"-l\" for a list of known databases, or \"-h\" for more information.")
+            exit(1)
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))

src/autobigs/cli/program.py

@@ -10,7 +10,7 @@ import importlib
 root_parser = argparse.ArgumentParser(epilog='Use "%(prog)s info -h" to learn how to get available MLST databases, and their available schemas.'
                                       + ' Once that is done, use "%(prog)s st -h" to learn how to retrieve MLST profiles.'
                                       )
-subparsers = root_parser.add_subparsers(required=True)
+subparsers = root_parser.add_subparsers(required=False)
 
 info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
 st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
@@ -33,6 +33,8 @@ def run():
               metadata.version("autoBIGS-engine")}.')
     if hasattr(args, "run"):
         args.run(args)
+    elif not args.version:
+        root_parser.print_usage()
 
 
 if __name__ == "__main__":

src/autobigs/cli/st.py

@@ -2,9 +2,9 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
 import datetime
-from autobigs.engine.data.local.csv import write_mlst_profiles_as_csv
-from autobigs.engine.data.local.fasta import read_multiple_fastas
-from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autobigs.engine.writing import write_mlst_profiles_as_csv
+from autobigs.engine.reading import read_multiple_fastas
+from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 
 def setup_parser(parser: ArgumentParser):
@@ -35,15 +35,6 @@ def setup_parser(parser: ArgumentParser):
         help="The output CSV name (.csv will be appended)."
     )
 
-    parser.add_argument(
-        "--exact", "-ex",
-        action="store_true",
-        dest="exact",
-        required=False,
-        default=False,
-        help="Should run exact matching rather than returning all similar ones"
-    )
-
     parser.add_argument(
         "--stop-on-fail", "-sof",
         action="store_true",
@@ -58,11 +49,11 @@ def setup_parser(parser: ArgumentParser):
 async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         gen_strings = read_multiple_fastas(args.fastas)
-        async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler:
-            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, exact=args.exact)
+        async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler:
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, args.stop_on_fail)
             failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
             if len(failed) > 0:
-                print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}")
+                print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")
             print(f"Completed fetching MLSTs for {len(args.fastas)} sequences.")
 
 def run_asynchronously(args):