From e3c64cfe1fd6a54036fa3e0f6cd6d205ab54cb59 Mon Sep 17 00:00:00 2001
From: Manuel Garcia <gilbert.mg22@gmail.com>
Date: Mon, 29 Apr 2024 13:15:25 +0200
Subject: [PATCH 1/5] Update authors in pyproject.toml

---
 pyproject.toml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 73de2c6..85f53f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,14 +5,15 @@ build-backend = "hatchling.build"
 [project]
 name = "fairly"
 version = "1.0.0"
-authors = [
-  { name="Serkan Girgin", email="s.girgin@utwente.nl" },
-  { name="Manuel Garcia Alvarez", email="m.g.garciaalvarez@tudelft.nl" },
-  { name="Jose Urra Llanusa", email="j.c.urrallanusa@tudelft.nl" }, ]
 description = "A package to create, publish, and download research datasets"
 readme = "README.rst"
 license = { file="LICENSE" }
 requires-python = ">=3.8"
+authors = [
+  { name="Serkan Girgin", email="s.girgin@utwente.nl" },
+  { name="Manuel Garcia Alvarez", email="m.g.garciaalvarez@tudelft.nl" },
+  { name="Jose Urra Llanusa", email="j.c.urrallanusa@tudelft.nl" }, 
+  ]
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",

From 731f9c546169b92889f75757929135ebbd9faf40 Mon Sep 17 00:00:00 2001
From: Manuel Garcia <gilbert.mg22@gmail.com>
Date: Mon, 29 Apr 2024 16:57:54 +0200
Subject: [PATCH 2/5] Refactor CLI module to remove unused import in
 __init__.py

---
 src/cli/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/cli/__init__.py b/src/cli/__init__.py
index 331197d..61e6063 100644
--- a/src/cli/__init__.py
+++ b/src/cli/__init__.py
@@ -1,5 +1,4 @@
 import sys
-import pprint as pp
 
 from ruamel.yaml import YAML
 import typer

From 1533e8d432c3ed63d33fc503bf720a360264b926 Mon Sep 17 00:00:00 2001
From: Manuel Garcia <gilbert.mg22@gmail.com>
Date: Mon, 29 Apr 2024 17:18:01 +0200
Subject: [PATCH 3/5] refactor package layout to 'src layout'

---
 pyproject.toml                   |   2 +-
 src/{ => fairly}/cli/__init__.py |  11 +-
 src/{ => fairly}/cli/config.py   |   0
 src/{ => fairly}/cli/dataset.py  | 274 +++++++++++++++----------------
 tests/test_cli.py                |   2 +-
 5 files changed, 143 insertions(+), 146 deletions(-)
 rename src/{ => fairly}/cli/__init__.py (91%)
 rename src/{ => fairly}/cli/config.py (100%)
 rename src/{ => fairly}/cli/dataset.py (96%)

diff --git a/pyproject.toml b/pyproject.toml
index 85f53f5..c14e558 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,4 +44,4 @@ dev = [
 "Funding" = "https://nwo.nl/en/researchprogrammes/open-science/open-science-fund"
 
 [project.scripts]
-fairly = "cli:app"
+fairly = "fairly.cli:app"
diff --git a/src/cli/__init__.py b/src/fairly/cli/__init__.py
similarity index 91%
rename from src/cli/__init__.py
rename to src/fairly/cli/__init__.py
index 61e6063..f857c16 100644
--- a/src/cli/__init__.py
+++ b/src/fairly/cli/__init__.py
@@ -3,15 +3,12 @@
 from ruamel.yaml import YAML
 import typer
 import fairly
-
-import cli.dataset
-import cli.config
-
-
+from fairly.cli import dataset
+from fairly.cli import config
 
 app = typer.Typer()
-app.add_typer(cli.dataset.app, name="dataset")
-app.add_typer(cli.config.app, name="config")
+app.add_typer(dataset.app, name="dataset")
+app.add_typer(config.app, name="config")
 
 @app.command()
 def list_repos():
diff --git a/src/cli/config.py b/src/fairly/cli/config.py
similarity index 100%
rename from src/cli/config.py
rename to src/fairly/cli/config.py
diff --git a/src/cli/dataset.py b/src/fairly/cli/dataset.py
similarity index 96%
rename from src/cli/dataset.py
rename to src/fairly/cli/dataset.py
index acfcdb2..25b7146 100644
--- a/src/cli/dataset.py
+++ b/src/fairly/cli/dataset.py
@@ -1,138 +1,138 @@
-import typer
-
-from rich.progress import Progress, SpinnerColumn, TextColumn
-
-import fairly
-
-
-app = typer.Typer(pretty_exceptions_show_locals=False)
-
-@app.command()
-def create(
-    path: str = typer.Argument(help="Path where the dataset will be created"),
-    template: str = typer.Option("default", help="Metadata template to be used for the dataset"),
-) -> None:
-    '''Create a local dataset under path with default template\n
-
-    fairly dataset create <path>\n
-
-    Create a local dataset under path with the specified template\n
-    <template> = 'zeondo, 4tu, default'\n
-
-    fairly dataset create <path> --template <template>
-    '''
-    fairly.init_dataset(path, template=template)
-
-
-@app.command()
-def clone(
-    id: str = typer.Argument(help="Dataset identifier (URL, DOI, or unique ID)"),
-    path: str = typer.Argument("", help="Path where the dataset will be stored"),
-    repo: str = typer.Option("", help="Repository option argument"),
-    token: str = typer.Option("", help="Access token option argument"),
-    notify: bool = typer.Option(False, help="Enable process notification"),
-    extract: bool = typer.Option(False, help="Extract archive files"),
-) -> None:
-    '''
-    Clones a dataset by using its URL address, DOI or unique ID.
-
-    Examples: \n
-        >>> fairly dataset clone <url|doi|uid> \n \n
-        >>> fairly dataset clone https://zenodo.org/records/7759648 \n
-        >>> fairly dataset clone 10.5281/zenodo.7759648 \n
-        >>> fairly dataset clone <repository> <id> \n
-        >>> fairly dataset clone --repo zenodo 7759648 \n
-    '''
-
-    if repo:
-        if token:
-            client = fairly.client(repo, token=token)
-        else:
-            client = fairly.client(repo)
-        dataset = client.get_dataset(id)
-
-    else:
-        dataset = fairly.dataset(id)
-
-    if not path:
-        path = dataset.doi if dataset.doi else "dataset"
-
-        for sep in ["/", "\\"]:
-            path = path.replace(sep, "_")
-
-    with Progress(
-        SpinnerColumn(),
-        TextColumn("[progress.description]{task.description}"),
-        transient = True,
-    ) as progress:
-        progress.add_task("Cloning dataset", total=None)
-
-        dataset.store(path, notify=fairly.notify if notify else None, extract=extract)
-        print(f"Dataset {id} is successfully cloned to {path}")
-
-
-    return None
-
-@app.command()
-def upload(
-    path: str = typer.Argument(help="Path where the dataset is located"),
-    repo: str = typer.Argument(help="Repository to upload the dataset"),
-    token: str = typer.Option(None, help="Access token option argument"),
-    notify: bool = typer.Option(False, help="Enable process notification"),
-):
-    '''
-    Uploads a local dataset to a data repository.
-    '''
-    dataset = fairly.dataset(path)
-
-    # TODO: Support repository selection from the metadata template of the dataset
-
-    if token:
-        client = fairly.client(repo, token=token)
-    else:
-        client = fairly.client(repo)
-
-    with Progress(
-        SpinnerColumn(),
-        TextColumn("[progress.description]{task.description}"),
-        transient = True,
-    ) as progress:
-        progress.add_task(description=f"Uploading dataset {path}", total=None)
-        remote_dataset = dataset.upload(client, notify=notify)
-
-    print(f"Dataset {path} is successfully uploaded at {remote_dataset.url or remote_dataset.plain_id}")
-
-
-@app.command()
-def delete(
-    id: str = typer.Argument(help="Dataset identifier (URL address, DOI, or unique ID)"),
-    repo: str = typer.Option("", help="Repository option argument"),
-    token: str = typer.Option("", help="Access token option argument"),
-):
-    '''
-    Deletes a dataset by using its URL address, DOI or unique ID.
-    '''
-    if repo:
-        if token:
-            client = fairly.client(repo, token=token)
-        else:
-            client = fairly.client(repo)
-        dataset = client.get_dataset(id)
-
-    else:
-        dataset = fairly.dataset(id)
-        client = dataset.client
-
-    with Progress(
-        SpinnerColumn(),
-        TextColumn("[progress.description]{task.description}"),
-        transient = True,
-    ) as progress:
-        progress.add_task(description=f"Deleting dataset {id}", total=None)
-        client.delete_dataset(dataset.id)
-
-    print(f"Dataset {id} is successfully deleted.")
-
-
-if __name__ == "__main__":
+import typer
+
+from rich.progress import Progress, SpinnerColumn, TextColumn
+
+import fairly
+
+
+app = typer.Typer(pretty_exceptions_show_locals=False)
+
+@app.command()
+def create(
+    path: str = typer.Argument(help="Path where the dataset will be created"),
+    template: str = typer.Option("default", help="Metadata template to be used for the dataset"),
+) -> None:
+    '''Create a local dataset under path with default template\n
+
+    fairly dataset create <path>\n
+
+    Create a local dataset under path with the specified template\n
+    <template> = 'zeondo, 4tu, default'\n
+
+    fairly dataset create <path> --template <template>
+    '''
+    fairly.init_dataset(path, template=template)
+
+
+@app.command()
+def clone(
+    id: str = typer.Argument(help="Dataset identifier (URL, DOI, or unique ID)"),
+    path: str = typer.Argument("", help="Path where the dataset will be stored"),
+    repo: str = typer.Option("", help="Repository option argument"),
+    token: str = typer.Option("", help="Access token option argument"),
+    notify: bool = typer.Option(False, help="Enable process notification"),
+    extract: bool = typer.Option(False, help="Extract archive files"),
+) -> None:
+    '''
+    Clones a dataset by using its URL address, DOI or unique ID.
+
+    Examples: \n
+        >>> fairly dataset clone <url|doi|uid> \n \n
+        >>> fairly dataset clone https://zenodo.org/records/7759648 \n
+        >>> fairly dataset clone 10.5281/zenodo.7759648 \n
+        >>> fairly dataset clone <repository> <id> \n
+        >>> fairly dataset clone --repo zenodo 7759648 \n
+    '''
+
+    if repo:
+        if token:
+            client = fairly.client(repo, token=token)
+        else:
+            client = fairly.client(repo)
+        dataset = client.get_dataset(id)
+
+    else:
+        dataset = fairly.dataset(id)
+
+    if not path:
+        path = dataset.doi if dataset.doi else "dataset"
+
+        for sep in ["/", "\\"]:
+            path = path.replace(sep, "_")
+
+    with Progress(
+        SpinnerColumn(),
+        TextColumn("[progress.description]{task.description}"),
+        transient = True,
+    ) as progress:
+        progress.add_task("Cloning dataset", total=None)
+
+        dataset.store(path, notify=fairly.notify if notify else None, extract=extract)
+        print(f"Dataset {id} is successfully cloned to {path}")
+
+
+    return None
+
+@app.command()
+def upload(
+    path: str = typer.Argument(help="Path where the dataset is located"),
+    repo: str = typer.Argument(help="Repository to upload the dataset"),
+    token: str = typer.Option(None, help="Access token option argument"),
+    notify: bool = typer.Option(False, help="Enable process notification"),
+):
+    '''
+    Uploads a local dataset to a data repository.
+    '''
+    dataset = fairly.dataset(path)
+
+    # TODO: Support repository selection from the metadata template of the dataset
+
+    if token:
+        client = fairly.client(repo, token=token)
+    else:
+        client = fairly.client(repo)
+
+    with Progress(
+        SpinnerColumn(),
+        TextColumn("[progress.description]{task.description}"),
+        transient = True,
+    ) as progress:
+        progress.add_task(description=f"Uploading dataset {path}", total=None)
+        remote_dataset = dataset.upload(client, notify=notify)
+
+    print(f"Dataset {path} is successfully uploaded at {remote_dataset.url or remote_dataset.plain_id}")
+
+
+@app.command()
+def delete(
+    id: str = typer.Argument(help="Dataset identifier (URL address, DOI, or unique ID)"),
+    repo: str = typer.Option("", help="Repository option argument"),
+    token: str = typer.Option("", help="Access token option argument"),
+):
+    '''
+    Deletes a dataset by using its URL address, DOI or unique ID.
+    '''
+    if repo:
+        if token:
+            client = fairly.client(repo, token=token)
+        else:
+            client = fairly.client(repo)
+        dataset = client.get_dataset(id)
+
+    else:
+        dataset = fairly.dataset(id)
+        client = dataset.client
+
+    with Progress(
+        SpinnerColumn(),
+        TextColumn("[progress.description]{task.description}"),
+        transient = True,
+    ) as progress:
+        progress.add_task(description=f"Deleting dataset {id}", total=None)
+        client.delete_dataset(dataset.id)
+
+    print(f"Dataset {id} is successfully deleted.")
+
+
+if __name__ == "__main__":
     app()
\ No newline at end of file
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 9f9ed2d..f80b0b9 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -5,7 +5,7 @@
 
 import re
 
-from cli import app
+from fairly.cli import app
 
 from typer.testing import CliRunner
 

From 0fd6afa8ffcfcb5ee886f7425d7a07f4f558e294 Mon Sep 17 00:00:00 2001
From: Manuel Garcia <gilbert.mg22@gmail.com>
Date: Mon, 29 Apr 2024 17:29:55 +0200
Subject: [PATCH 4/5] Add test_show_help function to test_cli.py

---
 tests/test_cli.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/test_cli.py b/tests/test_cli.py
index f80b0b9..ddab8aa 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,4 +1,5 @@
 import pytest
+import os
 from tests.conftest import *
 
 import fairly
@@ -11,6 +12,9 @@
 
 runner = CliRunner()
 
+def test_show_help():
+    exit_status = os.system("fairly --help")
+    assert exit_status == 0
 
 def test_show_config():
     result = runner.invoke(app, ["config", "show"])

From e7d2477f64972236ef7399f33aa59d94f24bb0fe Mon Sep 17 00:00:00 2001
From: Manuel Garcia <gilbert.mg22@gmail.com>
Date: Mon, 29 Apr 2024 17:31:09 +0200
Subject: [PATCH 5/5] Update cli test

---
 tests/test_cli.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_cli.py b/tests/test_cli.py
index ddab8aa..295b9ff 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -12,7 +12,8 @@
 
 runner = CliRunner()
 
-def test_show_help():
+def test_cli_help():
+    '''Test if CLI is reachable from the system terminal.'''
     exit_status = os.system("fairly --help")
     assert exit_status == 0