Merge pull request #162 from OSeMOSYS/develop

Release 1.0.1

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -0,0 +1,89 @@
+name: Bug Report
+description: File a bug report
+title: "[Bug]: <Replace with short description of bug>"
+labels: ["bug"]
+# assignees:
+#   - trevorb1
+body:
+
+  - type: textarea
+    attributes:
+      label: The Issue
+      description: A concise description of the issue you are experiencing.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Expected Behavior
+      description: A concise description of what you expected to happen.
+    validations:
+      required: false
+
+  - type: textarea
+    attributes:
+      label: Steps To Reproduce
+      description: How do you trigger this bug? Please walk us through it step by step.
+      placeholder: |
+        1. Running this command...
+        2. With this config.yaml file data...
+    validations:
+      required: false
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Log output
+      description: |
+        Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+        To include the full traceback error, run otoole in verbose mode with the "-v" flag
+      render: shell
+    validations:
+      required: false
+
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating System
+      description: What operating system are you running?
+      options:
+        - Linux
+        - MacOS
+        - Windows
+    validations:
+      required: true
+
+  - type: input
+    id: version
+    attributes:
+      label: What version of otoole are you running?
+      description: |
+        To check your version, use the command "otoole -V"
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Possible Solution
+      description: Do you have an idea on how to fix the issue?
+    validations:
+      required: false
+
+  - type: textarea
+    id: other
+    attributes:
+      label: Anything else?
+      description: |
+        Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
+    validations:
+      required: false
+
+  # - type: checkboxes
+  #   id: terms
+  #   attributes:
+  #     label: Code of Conduct
+  #     description: By submitting this issue, you agree to follow our [Code of Conduct](https://example.com)
+  #     options:
+  #       - label: I agree to follow this project's Code of Conduct
+  #         required: true

.github/ISSUE_TEMPLATE/docs.yaml

@@ -0,0 +1,53 @@
+name: Documentation
+description: Issues relating to documentation
+title: "[DOCS] <Replace with short description of documentation issue>"
+labels: ["documentation"]
+body:
+
+- type: dropdown
+  id: issuetype
+  attributes:
+    label: Type of documentation issue.
+    multiple: true
+    options:
+      - Missing Information
+      - Incorect Information
+      - Typo
+      - Other
+  validations:
+    required: true
+
+- type: textarea
+  id: description
+  attributes:
+    label: Issue Description
+    description: Detailed description of the documentation issue.
+    placeholder: |
+      ie. There is no description of how to convert from excel files
+  validations:
+    required: true
+
+- type: textarea
+  id: current
+  attributes:
+    label: Link to existing documentation
+    description: If applicable, provide the link to the current documentation location
+  validations:
+    required: false
+
+- type: textarea
+  id: solution
+  attributes:
+    label: Suggested Update
+    description: Do you have an idea on how to update the documention?
+  validations:
+    required: false
+
+- type: textarea
+  id: other
+  attributes:
+    label: Additional Info
+    description: |
+      Please provide any additional information to help fix this documentation issue.
+  validations:
+    required: false

.github/ISSUE_TEMPLATE/feature.yaml

@@ -0,0 +1,39 @@
+name: Feature request
+description: Ideas to improve the otoole
+title: "[FEATURE] <Replace with short description of feature request>"
+labels: ["enhancement"]
+body:
+
+- type: textarea
+  id: request
+  attributes:
+    label: Feature Request
+    description: Detailed description the suggested improvement
+  validations:
+    required: true
+
+- type: input
+  id: bug
+  attributes:
+    label: Is your feature related to a bug?
+    description: If applicable, refer to a an existing bug using the `#bugid` keyword
+    placeholder: "#bugid 10"
+  validations:
+    required: false
+
+- type: textarea
+  id: solution
+  attributes:
+    label: Suggested Solution
+    description: Do you have an idea on how to implement the idea?
+  validations:
+    required: false
+
+- type: textarea
+  id: other
+  attributes:
+    label: Additional Info
+    description: |
+      Please provide any additional information or resources that will help us implement the idea.
+  validations:
+    required: false

.github/pull_request_template.md

@@ -0,0 +1,12 @@
+<!--- Provide a short description of the pull request -->
+
+### Description
+<!--- Describe your changes in detail -->
+
+
+### Issue Ticket Number
+<!--- Link corresponding issue number -->
+
+
+### Documentation
+<!--- Where and how has this change been documented -->

.github/workflows/python.yaml

@@ -28,3 +28,9 @@ jobs:
       - name: Test with pytest
         run: |
           tox
+      - name: Upload coverage data to converalls.io
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          pip install --upgrade coveralls
+          coveralls --service=github

requirements.txt

@@ -4,7 +4,7 @@ flatten_dict
 importlib_resources; python_version<'3.7'
 networkx
 openpyxl
-pandas<2.0
+pandas
 pydantic
 pydot
 pyyaml

src/otoole/exceptions.py

@@ -72,18 +72,20 @@ def __str__(self):
         return f"{self.name} -> {self.message}"
 
 
-class OtooleExcelNameMismatchError(OtooleException):
-    """Name mismatch between config and excel tabs."""
+class OtooleNameMismatchError(OtooleException):
+    """Names not consistent between read in data and config file"""
 
     def __init__(
-        self, excel_name: str, message: str = "Excel tab name not found in config file"
+        self,
+        name: str,
+        message: str = "Name not consistent between data and config file",
     ) -> None:
-        self.excel_name = excel_name
+        self.name = name
         self.message = message
         super().__init__(self.message)
 
     def __str__(self):
-        return f"{self.excel_name} -> {self.message}"
+        return f"{self.name} -> {self.message}"
 
 
 class OtooleDeprecationError(OtooleException):
@@ -126,3 +128,45 @@ def __init__(
 
     def __str__(self):
         return f"{self.resource} -> {self.message}"
+
+
+class OtooleIndexError(OtooleException):
+    """Index data not consistent between data and config file
+
+    Arguments
+    ---------
+    resource : str
+        Name of the resource which is invalid
+    config_indices: List[str]
+        Indices from config file
+    data_indices: List[str]
+        Indices from input data
+    """
+
+    def __init__(self, resource, config_indices, data_indices):
+        self.resource = resource
+        self.config_indices = config_indices
+        self.data_indices = data_indices
+        self.message = "Indices inconsistent between config and data"
+
+    def __str__(self):
+        return f"{self.resource} -> {self.message}. Config indices are {self.config_indices}. Data indices are {self.data_indices}."
+
+
+class OtooleError(OtooleException):
+    """General purpose error
+
+    Arguments
+    ---------
+    resource : str
+        Name of the resource which is invalid
+    message : str
+        Error message
+    """
+
+    def __init__(self, resource, message):
+        self.resource = resource
+        self.message = message
+
+    def __str__(self):
+        return f"{self.resource} -> {self.message}"