From 9d3a89b56ff6dfa660b0b393c532c8a6d1242260 Mon Sep 17 00:00:00 2001
From: leej3 <johnleenimh@gmail.com>
Date: Tue, 25 Jun 2024 11:25:32 +0100
Subject: [PATCH] fix packaging and change name

---
 README.md                            |  2 +-
 {osm_cli => osm}/__init__.py         |  0
 {osm_cli => osm}/cli/main.py         |  2 +-
 {osm_cli => osm}/logging/__init__.py |  0
 {osm_cli => osm}/logging/logger.py   |  0
 {osm_cli => osm}/utils/__init__.py   |  0
 {osm_cli => osm}/utils/config.py     |  0
 pyproject.toml                       | 12 ++++++------
 tests/test_file_processing.py        |  2 +-
 tox.ini                              |  2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)
 rename {osm_cli => osm}/__init__.py (100%)
 rename {osm_cli => osm}/cli/main.py (90%)
 rename {osm_cli => osm}/logging/__init__.py (100%)
 rename {osm_cli => osm}/logging/logger.py (100%)
 rename {osm_cli => osm}/utils/__init__.py (100%)
 rename {osm_cli => osm}/utils/config.py (100%)

diff --git a/README.md b/README.md
index e536d1ef..f6e9ae5f 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.
 
 # How to setup and run the application
-- After cloning the repo, navigate into the project's root directory by running `cd osm_cli`
+- After cloning the repo, navigate into the project's root directory by running `cd osm`
 - Run `python -m venv venv` to create a Virtual Environment
 - Depending on your system, run the approriate command to Activate the Virtual Environment
 Windows: `venv\Scripts\activate`<br>
diff --git a/osm_cli/__init__.py b/osm/__init__.py
similarity index 100%
rename from osm_cli/__init__.py
rename to osm/__init__.py
diff --git a/osm_cli/cli/main.py b/osm/cli/main.py
similarity index 90%
rename from osm_cli/cli/main.py
rename to osm/cli/main.py
index b808b37b..92d9ed1a 100644
--- a/osm_cli/cli/main.py
+++ b/osm/cli/main.py
@@ -1,6 +1,6 @@
 import click
 
-from osm_cli.logging.logger import logger
+from osm.logging.logger import logger
 
 
 @click.group()
diff --git a/osm_cli/logging/__init__.py b/osm/logging/__init__.py
similarity index 100%
rename from osm_cli/logging/__init__.py
rename to osm/logging/__init__.py
diff --git a/osm_cli/logging/logger.py b/osm/logging/logger.py
similarity index 100%
rename from osm_cli/logging/logger.py
rename to osm/logging/logger.py
diff --git a/osm_cli/utils/__init__.py b/osm/utils/__init__.py
similarity index 100%
rename from osm_cli/utils/__init__.py
rename to osm/utils/__init__.py
diff --git a/osm_cli/utils/config.py b/osm/utils/config.py
similarity index 100%
rename from osm_cli/utils/config.py
rename to osm/utils/config.py
diff --git a/pyproject.toml b/pyproject.toml
index fb964d03..994f3e54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [project]
-name = "osm-cli"
+name = "osm"
 description = "Open Science Metrics (OSM) client for tracking scientific transparency and reproducibility metrics"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -30,21 +30,21 @@ dev = [
 
 [project.urls]
 homepage = "https://website"
-source = "https://github.com/nimh-dsst/osm-cli"
-issues = "https://github.com/nimh-dsst/osm-cli/issues"
+source = "https://github.com/nimh-dsst/osm"
+issues = "https://github.com/nimh-dsst/osm/issues"
 
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "osm_cli/_version.py"
+write_to = "osm/_version.py"
 
 [tool.setuptools.packages.find]
-where = ["osm_cli"]
+where = ["."]
 
 [project.scripts]
-osm-cli = "osm_cli.cli.main:osm"
+osm = "osm.cli.main:osm"
 
 [tool.black]
 line-length = 88
diff --git a/tests/test_file_processing.py b/tests/test_file_processing.py
index 9f6eda9b..b3318168 100644
--- a/tests/test_file_processing.py
+++ b/tests/test_file_processing.py
@@ -3,7 +3,7 @@
 import pytest
 from click.testing import CliRunner
 
-from osm_cli.cli.main import pdf_xml
+from osm.cli.main import pdf_xml
 
 
 @pytest.fixture
diff --git a/tox.ini b/tox.ini
index aba50e48..4420e676 100644
--- a/tox.ini
+++ b/tox.ini
@@ -5,7 +5,7 @@ envlist = py39, py310, py311, py312, lint, format
 deps =
     .[dev]
 commands =
-    python -m pytest --cov=osm_cli --cov-report=term-missing --cov-report=html --cov-report=xml
+    python -m pytest --cov=osm --cov-report=term-missing --cov-report=html --cov-report=xml
 
 [testenv:lint]
 description = Run ruff to lint the code