Merge branch 'release/0.11.0'

First PyOpenSci approved version.

.all-contributorsrc

@@ -0,0 +1,122 @@
+{
+  "projectName": "rdata",
+  "projectOwner": "VNMabus",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "files": [
+    "CONTRIBUTORS.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "commitConvention": "none",
+  "contributors": [
+    {
+      "login": "vnmabus",
+      "name": "Carlos Ramos Carreño",
+      "avatar_url": "https://avatars.githubusercontent.com/u/2364173?v=4",
+      "profile": "https://github.com/vnmabus",
+      "contributions": [
+        "code",
+        "data",
+        "doc",
+        "example",
+        "ideas",
+        "infra",
+        "maintenance",
+        "projectManagement",
+        "question",
+        "review",
+        "test",
+        "tutorial"
+      ]
+    },
+    {
+      "login": "",
+      "name": "CSC - IT Center for Science Ltd",
+      "avatar_url": "https://avatars.githubusercontent.com/u/5947494?v=4",
+      "profile": "https://www.csc.fi",
+      "contributions": [
+        {
+          "type": "code",
+          "url": "https://github.com/vnmabus/rdata/commits?author=trossi"
+        }
+      ]
+    },
+    {
+      "login": "trossi",
+      "name": "Tuomas Rossi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/34502776?v=4",
+      "profile": "https://github.com/trossi",
+      "contributions": [
+        "code",
+        "ideas",
+        "bug"
+      ]
+    },
+    {
+      "login": "VolodyaCO",
+      "name": "Vladimir Vargas-Calderón",
+      "avatar_url": "https://avatars.githubusercontent.com/u/31494271?v=4",
+      "profile": "https://www.researchgate.net/profile/Vladimir_Vargas-Calderon",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "Jorgelindo238",
+      "name": "Jorgelindo",
+      "avatar_url": "https://avatars.githubusercontent.com/u/79350063?v=4",
+      "profile": "https://jorgelindodaveiga.myportfolio.com/",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "zoj613",
+      "name": "zoj613",
+      "avatar_url": "https://avatars.githubusercontent.com/u/44142765?v=4",
+      "profile": "https://github.com/zoj613",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "schlegelp",
+      "name": "Philipp Schlegel",
+      "avatar_url": "https://avatars.githubusercontent.com/u/7161148?v=4",
+      "profile": "https://github.com/schlegelp",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "deeenes",
+      "name": "deeenes",
+      "avatar_url": "https://avatars.githubusercontent.com/u/2679889?v=4",
+      "profile": "https://denes.omnipathdb.org/",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "soheila-sahami",
+      "name": "Soheila",
+      "avatar_url": "https://avatars.githubusercontent.com/u/9429831?v=4",
+      "profile": "https://github.com/soheila-sahami",
+      "contributions": [
+        "ideas"
+      ]
+    },
+    {
+      "login": "userLUX",
+      "name": "userLUX",
+      "avatar_url": "https://avatars.githubusercontent.com/u/107994632?v=4",
+      "profile": "https://github.com/userLUX",
+      "contributions": [
+        "bug"
+      ]
+    }
+  ],
+  "contributorsPerLine": 7,
+  "linkToUsage": true
+}

.gitattributes

@@ -0,0 +1,5 @@
+# Mark rda and rds files as binary.
+# Otherwise git might change the line endings of
+# ascii-formatted files, which breaks the tests
+*.rda -text
+*.rds -text

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,101 @@
+name: Bug report
+description: Create a report to help us reproduce and fix a bug
+labels: [bug]
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      #### Please check that the bug has not been previously notified before submitting, by searching through the [issues list](https://github.com/vnmabus/rdata/issues).
+- type: textarea
+  attributes:
+    label: Bug description summary
+    description: >
+      Please describe the bug in a brief paragraph(s). Be clear and concise.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Code to reproduce the bug
+    description: |
+      Please add a minimal code example that can reproduce the error. If the bug does not require more code than loading a data file you can leave this empty. This will be automatically converted to a Python block.
+    placeholder: |
+      import rdata
+
+      parsed = rdata.parser.parse_file("data.rda")
+      converted = rdata.conversion.convert(parsed)
+      converted
+    render: Python
+- type: textarea
+  attributes:
+    label: Data file(s)
+    description: >
+      If the bug was caused by loading a particular data file, please attach it or paste a link to it here.
+- type: textarea
+  attributes:
+    label: Expected result
+    description: >
+      Paste or describe the result that you expected here.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Actual result
+    description: >
+      Paste or describe the result that you obtained here. If the code raises an error, you can past it in the next field.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Traceback (if an exception is raised)
+    description: |
+      If an exception is raised, copy and paste the traceback here.
+    placeholder: |
+      FileNotFoundError                         Traceback (most recent call last)
+      Cell In[5], line 3
+            1 import rdata
+      ----> 3 parsed = rdata.parser.parse_file("data.rda")
+            4 converted = rdata.conversion.convert(parsed)
+            5 converted
+      
+      File .../rdata/parser/_parser.py:1139, in parse_file(file_or_path, expand_altrep, altrep_constructor_dict, extension)
+         1137     if extension is None:
+         1138         extension = getattr(path, "suffix", None)
+      -> 1139     data = path.read_bytes()
+         1141 return parse_data(
+         1142     data,
+         1143     expand_altrep=expand_altrep,
+         1144     altrep_constructor_dict=altrep_constructor_dict,
+         1145     extension=extension,
+         1146 )
+      
+      File .../pathlib.py:1050, in Path.read_bytes(self)
+         1046 def read_bytes(self):
+         1047     """
+         1048     Open the file in bytes mode, read it, and close the file.
+         1049     """
+      -> 1050     with self.open(mode='rb') as f:
+         1051         return f.read()
+      
+      File .../pathlib.py:1044, in Path.open(self, mode, buffering, encoding, errors, newline)
+         1042 if "b" not in mode:
+         1043     encoding = io.text_encoding(encoding)
+      -> 1044 return io.open(self, mode, buffering, encoding, errors, newline)
+      
+      FileNotFoundError: [Errno 2] No such file or directory: 'data.rda'
+    render: Python
+- type: textarea
+  attributes:
+    label: Software versions
+    description: >
+      Include the version of the library used (obtained with `rdata.__version__`). If relevant, you can include here the OS version and versions of related software.
+    placeholder: |
+      rdata version: 0.10.0
+      OS: Windows 10
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Additional context
+    description: >
+      Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,35 @@
+name: Feature request
+description: Suggest an idea for this project
+labels: [enhancement]
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      #### Please check that this idea has not been proposed previously, by searching through the [issues list](https://github.com/vnmabus/rdata/issues).
+- type: textarea
+  attributes:
+    label: Motivation
+    description: >
+      A clear and concise description of what the problem is. Ex. I am always frustrated when [...]
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Desired functionality
+    description: >
+      A clear and concise description of what you want to happen.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Alternatives
+    description: >
+      A clear and concise description of any alternative solutions or features you have considered.
+  validations:
+    required: false
+- type: textarea
+  attributes:
+    label: Additional context
+    description: >
+      Add any other context about the problem here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,31 @@
+<!--
+Thanks for your contribution! Please ensure you have taken a look at
+the contribution guidelines:
+https://github.com/vnmabus/rdata/blob/develop/CONTRIBUTING.md
+-->
+
+## References to issues or other PRs
+<!--
+Include links to the relevant issues and PRs, using the relevant Github
+keywords (e.g., Fixes) for closing automatically the issues resolved
+on merge (see https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue).
+If there is no current issue discussing the addition of this functionality, it
+is recommended to create one and discuss the feature there.
+Otherwise, it is possible for this functionality to be rejected, or to require
+considerable changes.
+Example: Fixes #42. See also #123.
+-->
+
+
+## Describe the proposed changes
+
+
+## Additional information
+
+
+## Checklist before requesting a review
+
+- [ ] I have performed a self-review of my code
+- [ ] The code conforms to the style used in this package (checked with [Ruff](https://docs.astral.sh/ruff/))
+- [ ] The code is fully documented and typed (type-checked with [Mypy](https://mypy-lang.org/))
+- [ ] I have added thorough tests for the new/changed functionality

.github/workflows/main.yml

@@ -11,13 +11,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/mypy.yml

@@ -0,0 +1,30 @@
+name: Mypy
+
+on:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Mypy
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install dependencies
+      run: |
+        pip3 install ".[test,typing]" mypy;
+        rm -rf build;  
+ 
+    - uses: tsuyoshicho/action-mypy@v4
+      with:
+        github_token: ${{ secrets.github_token }}
+        reporter: github-pr-review
+        install_types: false
+        # The action will output fail if there are mypy errors
+        level: error
+        filter_mode: nofilter

.github/workflows/python-publish.yml

@@ -21,9 +21,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/ruff.yml

@@ -0,0 +1,10 @@
+name: Ruff
+on: [push]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: check --output-format github

.gitignore

@@ -102,3 +102,6 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+# ruff
+/.ruff_cache/