fix: Fix initial linter issues

.github/CODE_OF_CONDUCT.md

@@ -2,45 +2,74 @@
 
 ## Our Pledge
 
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual identity
+and orientation.
 
 ## Our Standards
 
-Examples of behavior that contributes to creating a positive environment include:
+Examples of behavior that contributes to creating a positive environment
+include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 
-Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
 
-Project maintainers 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, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+Project maintainers 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, or to ban temporarily or permanently any
+contributor for other behaviors that they deem inappropriate, threatening,
+offensive, or harmful.
 
 ## Scope
 
-This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. The
+project team will review and investigate all complaints, and will respond in a
+way that it deems appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an
+incident. Further details of specific enforcement policies may be posted
+separately.
 
-Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
 
 [homepage]: http://contributor-covenant.org
 [version]: http://contributor-covenant.org/version/1/4/

.github/CONTRIBUTING.md

@@ -3,10 +3,19 @@
 > Alone we can do so little; together we can do so much. — Helen Keller
 
 ## Testing
+
 TBD
 
 ## Code conventions
-All code is formatted with the Black code formatter. This leaves little room for discussion on the code conventions and helps us focus on the actual quality of the code. More information on the Black formatter can be found here: [Python Black](https://github.com/ambv/black)
+
+All code is formatted with the Black code formatter. This leaves little room for
+discussion on the code conventions and helps us focus on the actual quality of
+the code. More information on the Black formatter can be found here:
+[Python Black](https://github.com/ambv/black)
 
 ## Submitting changes
-Any changes have to be commit to a feature branch and can only get into the master branch through an approved pull request. Please provide clear commit messages and pull requests so the reviewer knows what has changed and what the impact / effect is.
+
+Any changes have to be commit to a feature branch and can only get into the
+master branch through an approved pull request. Please provide clear commit
+messages and pull requests so the reviewer knows what has changed and what the
+impact / effect is.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,28 +1,25 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+**Describe the bug** A clear and concise description of what the bug is.
+
+**To Reproduce** Steps to reproduce the behavior:
 
-**To Reproduce**
-Steps to reproduce the behavior:
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
 4. See error
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+**Expected behavior** A clear and concise description of what you expected to
+happen.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+**Screenshots** If applicable, add screenshots to help explain your problem.
 
 **Environment (please complete the following information):**
- - OS: [e.g. Windows / Linux]
- - Version [e.g. Python 3.7.0]
 
-**Additional context**
-Add any other context about the problem here.
+- OS: [e.g. Windows / Linux]
+- Version [e.g. Python 3.7.0]
+
+**Additional context** Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +1,16 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-
 ---
 
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+**Is your feature request related to a problem? Please describe.** A clear and
+concise description of what the problem is. Ex. I'm always frustrated when [...]
 
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
+**Describe the solution you'd like** A clear and concise description of what you
+want to happen.
 
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
+**Describe alternatives you've considered** A clear and concise description of
+any alternative solutions or features you've considered.
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+**Additional context** Add any other context or screenshots about the feature
+request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,8 @@
 ### All Submissions:
 
-* [ ] Have you followed the guidelines in our Contributing document?
-* [ ] Have you checked to ensure there aren't other open [Pull Requests](../../pulls) for the same update/change?
+- [ ] Have you followed the guidelines in our Contributing document?
+- [ ] Have you checked to ensure there aren't other open
+      [Pull Requests](../../pulls) for the same update/change?
 
 ### New Feature Submissions:
 
@@ -10,6 +11,7 @@
 
 ### Changes to Core Features:
 
-* [ ] Have you added an explanation of what your changes do and why you'd like us to include them?
-* [ ] Have you written new tests for your core changes, as applicable?
-* [ ] Have you successfully ran tests with your changes locally?
+- [ ] Have you added an explanation of what your changes do and why you'd like
+      us to include them?
+- [ ] Have you written new tests for your core changes, as applicable?
+- [ ] Have you successfully ran tests with your changes locally?

.gitignore

@@ -104,6 +104,7 @@ venv.bak/
 .mypy_cache/
 .ruff_cache/
 
+.vscode/
 DSS.egg-info/
 test-reports/
 .coveragerc

.pre-commit-config.yaml

@@ -32,8 +32,7 @@ repos:
         language: system
         exclude: |
           (?x)(
-            docs|
-            tests
+            docs
           )
         pass_filenames: true
         types:
@@ -48,7 +47,7 @@ repos:
         exclude: |
           (?x)(
             docs|
-            tests
+            examples|
           )
         types:
           - python

LICENCE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

README.md

@@ -1,20 +1,30 @@
-> PyMedX is a fork from a archived project called PyMed: https://github.com/gijswobben/pymedx
+> PyMedX is a fork from a archived project called PyMed:
+> https://github.com/gijswobben/pymedx
 
 # PyMedX - PubMed Access through Python
-PyMedX is a Python library that provides access to PubMed through the PubMed API.
+
+PyMedX is a Python library that provides access to PubMed through the PubMed
+API.
 
 ## Why this library?
-The PubMed API is not very well documented and querying it in a performant way is too complicated and time consuming for researchers. This wrapper provides access to the API in a consistent, readable and performant way.
+
+The PubMed API is not very well documented and querying it in a performant way
+is too complicated and time consuming for researchers. This wrapper provides
+access to the API in a consistent, readable and performant way.
 
 ## Features
+
 This library takes care of the following for you:
 
 - Querying the PubMed database (with the standard PubMed query language)
 - Batching of requests for better performance
 - Parsing and cleaning of the retrieved articles
 
 ## Examples
-For full (working) examples have a look at the `examples/` folder in this repository. In essence you only need to import the `PubMed` class, instantiate it, and use it to query:
+
+For full (working) examples have a look at the `examples/` folder in this
+repository. In essence you only need to import the `PubMed` class, instantiate
+it, and use it to query:
 
 ```python
 from pymedx import PubMed
@@ -23,12 +33,22 @@ results = pubmed.query("Some query", max_results=500)
 ```
 
 ## Notes on the API
-The original documentation of the PubMed API can be found here: [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/tools/developers/). PubMed Central kindly requests you to:
+
+The original documentation of the PubMed API can be found here:
+[PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/tools/developers/). PubMed
+Central kindly requests you to:
 
 > - Do not make concurrent requests, even at off-peak times; and
-> - Include two parameters that help to identify your service or application to our servers
->   * _tool_ should be the name of the application, as a string value with no internal spaces, and
->   * _email_ should be the e-mail address of the maintainer of the tool, and should be a valid e-mail address.
+> - Include two parameters that help to identify your service or application to
+>   our servers
+>   - _tool_ should be the name of the application, as a string value with no
+>     internal spaces, and
+>   - _email_ should be the e-mail address of the maintainer of the tool, and
+>     should be a valid e-mail address.
 
 ## Notice of Non-Affiliation and Disclaimer
-The author of this library is not affiliated, associated, authorized, endorsed by, or in any way officially connected with PubMed, or any of its subsidiaries or its affiliates. The official PubMed website can be found at https://www.ncbi.nlm.nih.gov/pubmed/.
+
+The author of this library is not affiliated, associated, authorized, endorsed
+by, or in any way officially connected with PubMed, or any of its subsidiaries
+or its affiliates. The official PubMed website can be found at
+https://www.ncbi.nlm.nih.gov/pubmed/.