Added bioconda and personal conda repos to channels

.devcontainer/Dockerfile

@@ -0,0 +1,16 @@
+FROM mcr.microsoft.com/devcontainers/miniconda:1-3
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment to install a different version of Python than the default
+# RUN conda install -y python=3.6 \
+#     && pip install --no-cache-dir pipx \
+#     && pipx reinstall-all
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -1,9 +1,11 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/python
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
 {
-	"name": "Python 3",
-	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+	"name": "Miniconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	},
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -12,7 +14,9 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt && pip install -e .",
+	"postCreateCommand": "pip install -e .",
+
+	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
 			"extensions": [
@@ -20,8 +24,6 @@
 			]
 		}
 	},
-	// Configure tool-specific properties.
-	// "customizations": {},
 
 	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
 	// "remoteUser": "root"

.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file is copied into the container along with environment.yml* from the
+parent folder. This is done to prevent the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

Jenkinsfile

@@ -2,14 +2,16 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'pip'
-            inheritFrom 'pip'
+            defaultContainer 'miniforge3'
+            inheritFrom 'miniforge'
         }
     }
     stages {
         stage("install") {
             steps {
-                sh 'python -m pip install -r requirements.txt'
+                sh 'conda config --add channels bioconda'
+                sh 'conda config --add channels https://git.reslate.systems/api/packages/ydeng/conda'
+                sh 'conda env update -n base -f environment.yml'
             }
         }
         stage("unit tests") {
@@ -22,11 +24,14 @@ pipeline {
         stage("build") {
             steps {
                 sh "python -m build"
+                sh "grayskull pypi dist/*.tar.gz --maintainers 'Harrison Deng'"
+                sh "python scripts/patch_recipe.py"
+                sh 'conda build autobigs-cli -c bioconda --output-folder conda-bld --verify'
             }
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl, conda-bld/**/*.conda', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
@@ -42,6 +47,7 @@ pipeline {
                     }
                     steps {
                         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/*'
+                        sh 'curl --user ${CREDS_USR}:${CREDS_PSW} --upload-file conda-bld/**/*.conda https://git.reslate.systems/api/packages/${CREDS_USR}/conda/$(basename conda-bld/**/*.conda)'
                     }
                 }
                 stage ("pypi.org") {

environment.yml

@@ -0,0 +1,14 @@
+name: base
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - pytest
+  - pytest-asyncio
+  - pytest-cov
+  - python-build
+  - conda-build
+  - twine==6.0.1
+  - setuptools_scm
+  - grayskull
+  - curl

pyproject.toml

@@ -6,7 +6,7 @@ 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==0.12.*"
 ]
@@ -14,8 +14,8 @@ 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]

scripts/patch_recipe.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+
+import argparse
+from os import fdopen, path
+import os
+import re
+import shutil
+from sys import argv
+import tempfile
+
+INDENTATION = "  "
+GRAYSKULL_OUTPUT_PATH = "autoBIGS.cli"
+RUN_EXPORTED_VALUE = r'{{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}'
+LICENSE_SUFFIX = "-or-later"
+HOME_PAGE = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli"
+
+def _calc_indentation(line: str):
+    return len(re.findall(INDENTATION, line.split(line.strip())[0])) if line != "\n" else 0
+
+def read_grayskull_output():
+    original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
+    original_meta = path.join(original_recipe, "meta.yaml")
+    meta_file = open(original_meta)
+    lines = meta_file.readlines()
+    meta_file.close()
+    return lines
+
+def update_naming_scheme(lines):
+    modified_lines = []
+    for line in lines:
+        matches = re.finditer(r"\{\{\s*name\|lower()\s+\}\}", line)
+        modified_line = line
+        for match in matches:
+            modified_line = modified_line[:match.start(1)] + r'|replace(".", "-")' + modified_line[match.end(1):]
+        modified_lines.append(modified_line)
+    return modified_lines
+
+def inject_run_exports(lines: list[str]):
+    package_indent = False
+    modified_lines = []
+    for line in lines:
+        indentation_count = _calc_indentation(line)
+        if line == "build:\n" and indentation_count == 0:
+            package_indent = True
+            modified_lines.append(line)
+        elif package_indent and indentation_count == 0:
+            modified_lines.append(INDENTATION*1 + "run_exports:\n")
+            modified_lines.append(INDENTATION*2 + "- " + RUN_EXPORTED_VALUE + "\n")
+            package_indent = False
+        else:
+            modified_lines.append(line)
+    return modified_lines
+
+def suffix_license(lines: list[str]):
+    about_indent = False
+    modified_lines = []
+    for line in lines:
+        indentation_count = _calc_indentation(line)
+        if line == "about:\n" and indentation_count == 0:
+            about_indent = True
+            modified_lines.append(line)
+        elif about_indent and indentation_count == 1 and line.lstrip().startswith("license:"):
+            modified_lines.append(line.rstrip() + LICENSE_SUFFIX  + "\n")
+            about_indent = False
+        else:
+            modified_lines.append(line)
+    return modified_lines
+
+def inject_home_page(lines: list[str]):
+    about_indent = False
+    modified_lines = []
+    for line in lines:
+        indentation_count = _calc_indentation(line)
+        if line == "about:\n" and indentation_count == 0:
+            about_indent = True
+            modified_lines.append(line)
+        elif about_indent and indentation_count == 0:
+            modified_lines.append(INDENTATION + "home: " + HOME_PAGE + "\n")
+            about_indent = False
+        else:
+            modified_lines.append(line)
+    return modified_lines
+
+def write_to_original(lines: list[str]):
+    original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
+    original_meta = path.join(original_recipe, "meta.yaml")
+    with open(original_meta, "w") as file:
+        file.writelines(lines)
+
+def rename_recipe_dir():
+    new_recipe_name = path.abspath(path.join(GRAYSKULL_OUTPUT_PATH.replace(".", "-").lower()))
+    shutil.rmtree(new_recipe_name, ignore_errors=True)
+    os.replace(path.abspath(GRAYSKULL_OUTPUT_PATH), new_recipe_name)
+
+if __name__ == "__main__":
+    original_grayskull_out = read_grayskull_output()
+    modified_recipe_meta = None
+    modified_recipe_meta = update_naming_scheme(original_grayskull_out)
+    modified_recipe_meta = inject_run_exports(modified_recipe_meta)
+    modified_recipe_meta = suffix_license(modified_recipe_meta)
+    modified_recipe_meta = inject_home_page(modified_recipe_meta)
+    write_to_original(modified_recipe_meta)
+    rename_recipe_dir()

src/autobigs/cli/info.py

@@ -27,7 +27,7 @@ def setup_parser(parser: ArgumentParser):
     )
 
     parser.add_argument(
-        "--csv-prefix", "-o",
+        "--csv", "-o",
         dest="csv_output",
         required=False,
         default=None,
@@ -39,18 +39,21 @@ def setup_parser(parser: ArgumentParser):
 
 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)
             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:
-                dbs_csv_path = path.splitext(args.csv_output)[0] + "_" + "dbs.csv"
-                with open(dbs_csv_path, "w") as csv_out_handle:
+                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(dbs_csv_path))
+                    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)
@@ -58,14 +61,15 @@ async def run(args: Namespace):
             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:
-                schema_csv_path = path.splitext(args.csv_output)[0] + "_" + "schemas.csv"
-                with open(schema_csv_path, "w") as csv_out_handle:
+                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(schema_csv_path))
+                    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\" for a list of known databases, or \"-h\" for more information.")
+            exit(1)
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))