Update Documentation

.gitignore

@@ -10,3 +10,4 @@ dist
 tmp
 .ipynb_checkpoints
 /tests/non_rdm_repo/
+.vscode

.readthedocs.yaml

@@ -5,23 +5,19 @@
 # Required
 version: 2
 
-# Set the version of Python and other tools you might need
+# Set the version of Python and other tools that might be needed
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: "mambaforge-4.10"
+    python: "mambaforge-latest"
+  jobs:
+    install:
+      - pip install .[all] --group docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/source/conf.py
+  configuration: docs/source/conf.py
 
-# Optionally declare the Python requirements required to build your docs
+# Optionally declare the Python requirements required to build the docs
 conda:
   environment: environment.yml
-
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs

AUTHORS.md

@@ -0,0 +1,8 @@
+# Contributors
+
+* [Ronald Jäpel](https://github.com/ronald-jaepel) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Hannah Lanzrath](https://github.com/hannahlanzrath) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Johannes Schmölder](https://github.com/schmoelder) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Katharina Paul](https://github.com/katharinapaul2403) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Daniel Klauß](https://github.com/daklauss) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Eric von Lieres](https://github.com/lieres) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, - Germany)

CITATION.bib

@@ -0,0 +1,2 @@
+% As an open-source project, CADET-RDM relies on the support and recognition from users and researchers to thrive.
+% Therefore, we kindly ask that any publications or projects leveraging the capabilities of CADET-RDM acknowledge its creators and their contributions by citing an adequate selection of our publications.

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+cadet@fz-juelich.de.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

README.md

@@ -2,7 +2,7 @@
 
 Welcome to CADET-RDM, a project by the Forschungszentrum Jülich.
 
-This tool aims to help track and version control:
+This toolbox aims to help track and version control:
 - input data
 - code
 - software versions
@@ -12,4 +12,5 @@ and allow for easy sharing, integration, and reproduction of generated results.
 
 ## Documentation
 
-You can read the documentation [here](https://cadet-rdm.readthedocs.io).
+The documentation contains a user guide with helpful information on how to install CADET-RDM, how to quickly start working with it and a more detailed explaination of its tools.
+The documentation can be found [here](https://cadet-rdm.readthedocs.io).

SECURITY.md

@@ -0,0 +1,17 @@
+# Security Policy
+
+## 1. No Network Dependencies
+
+CADET operates entirely offline and does not require any network access, nor does it handle sensitive information such as personal identifiers. This eliminates common attack vectors like network exploits or data breaches.
+
+## 2. Code Integrity and Contribution Reviews
+
+While there are no significant security risks associated with using CADET, we maintain strict controls over our source code. Any external contributions to the project are thoroughly reviewed and must meet our contribution guidelines. All pull requests are checked to ensure they do not introduce vulnerabilities.
+
+## 3. Dependency Management
+
+CADET does not rely on third-party libraries that introduce network or verification components. We carefully manage dependencies to ensure they are up-to-date and secure.
+
+## 4. Reporting Vulnerabilities
+
+Though CADET does not involve typical security risks, we encourage users and contributors to report any unexpected behavior or potential vulnerabilities they may discover. Please contact us via cadet@fz-juelich.de if you believe you've found a security issue.

cadetrdm/cli_integration.py

@@ -13,30 +13,30 @@ def cli():
 
 
 @cli.command(help="Create an empty CADET-RDM repository or initialize over an existing git repo.")
-@click.option('--output_repo_name', default="output",
-              help='Name of the folder where the tracked output should be stored. Optional. Default: "output".')
+@click.option('--output_directory_name', default="output",
+              help='Name of the directory where the tracked output should be stored. Optional. Default: "output".')
 @click.option('--gitignore', default=None,
               help='List of files to be added to the gitignore file. Optional.')
 @click.option('--gitattributes', default=None,
               help='List of files to be added to the gitattributes file. Optional.')
 @click.option('--cookiecutter', default=None,
               help='URL or path to cookiecutter template. Optional.')
 @click.argument('path_to_repo', required=False)
-def init(path_to_repo: str = None, output_repo_name: (str | bool) = "output", gitignore: list = None,
+def init(path_to_repo: str = None, output_directory_name: (str | bool) = "output", gitignore: list = None,
          gitattributes: list = None, cookiecutter: str = None, output_repo_kwargs: dict = None):
     if path_to_repo is None:
         path_to_repo = "."
     from cadetrdm.initialize_repo import initialize_repo as initialize_git_repo_implementation
-    initialize_git_repo_implementation(path_to_repo, output_repo_name, gitignore,
+    initialize_git_repo_implementation(path_to_repo, output_directory_name, gitignore,
                                        gitattributes, output_repo_kwargs, cookiecutter)
 
 
-@cli.command(help="Clone a repository into a new d^irectory.")
+@cli.command(help="Clone a repository into a new empty directory.")
 @click.argument('project_url')
-@click.argument('dest', required=False)
-def clone(project_url, dest: str = None):
+@click.argument('destination_path', required=False)
+def clone(project_url, destination_path: str = None):
     from cadetrdm import ProjectRepo
-    repo = ProjectRepo.clone(url=project_url, to_path=dest)
+    repo = ProjectRepo.clone(url=project_url, to_path=destination_path)
     del repo
 
 

cadetrdm/container/ApptainerAdapter.py

@@ -61,7 +61,7 @@
 #
 #         ssh_location = Path.home() / ".ssh"
 #         if not ssh_location.exists():
-#             raise FileNotFoundError("No ssh folder found. Please report this on GitHub/CADET/CADET-RDM")
+#             raise FileNotFoundError("No ssh directory found. Please report this on GitHub/CADET/CADET-RDM")
 #
 #         container = self.client.containers.run_yml(
 #             image=image,

cadetrdm/container/containerAdapter.py

@@ -45,7 +45,7 @@ def _prepare_case_command(case, command, container_options_filename):
         if command_install is not None:
             commands.append(command_install)
 
-        # pull the study from the URL into a "study" folder
+        # pull the study from the URL into a "study" repository
         command_pull = f"rdm clone {case.project_repo.url} study"
         # cd into the "study" folder
         command_cd = "cd study"

cadetrdm/container/dockerAdapter.py

@@ -72,7 +72,7 @@ def _run_command(self, full_command, image, mounts=None):
 
         ssh_location = Path.home() / ".ssh"
         if not ssh_location.exists():
-            raise FileNotFoundError("No ssh folder found. Please report this on GitHub/CADET/CADET-RDM")
+            raise FileNotFoundError("No ssh directory found. Please report this on GitHub/CADET/CADET-RDM")
 
         volumes = {
             f"{Path.home()}/.ssh": {'bind': "/root/.ssh_host_os", 'mode': "ro"},

cadetrdm/container/podmanAdapter.py

@@ -69,7 +69,7 @@ def _run_command(self, full_command, image, mounts=None):
 
         ssh_location = Path.home() / ".ssh"
         if not ssh_location.exists():
-            raise FileNotFoundError("No ssh folder found. Please report this on GitHub/CADET/CADET-RDM")
+            raise FileNotFoundError("No ssh directory found. Please report this on GitHub/CADET/CADET-RDM")
 
         full_command = full_command.replace('"', "'")
 
@@ -82,7 +82,7 @@ def _run_command(self, full_command, image, mounts=None):
         podman_command = (
             f'podman run '
             '--rm '  # remove container after run_yml (to keep space usage low)
-            f'-v {ssh_location}:/root/.ssh_host_os:ro '  # mount ssh folder for the container to access
+            f'-v {ssh_location}:/root/.ssh_host_os:ro '  # mount ssh directory for the container to access
             f'{volume_mounts}'  # mount options file
             f'{image} '  # specify image name
             f'bash -c "{full_command}"'  # run_yml command in bash shell