Add typos and fix typos

.pre-commit-config.yaml

@@ -10,3 +10,7 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: debug-statements
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.23.1
+    hooks:
+      - id: typos

.typos.toml

@@ -0,0 +1,9 @@
+[default.extend-words]
+ba = "ba"
+strat = "strat"
+whe = "whe"
+mis = "mis"
+hassel = "hassel"
+Hassel = "Hassel"
+noy = "noy"
+pn = "pn"

README.md

@@ -14,14 +14,14 @@ your updates will be visible at `https://protocol.isimip.org`.
 As a rule, the sector-specific text should be kept to a minimum and cover
 as much structure as possible by machine-readable code under [definitions](definitions/).
 
-The React JavaScript app is build in a seperate step which are described under [app/README.md]([app/README.md]).
+The React JavaScript app is build in a separate step which are described under [app/README.md]([app/README.md]).
 
 Setup
 -----
 
 Building the protocol needs git and a recent Python version (> 3.6). The installation of Python (and its developing packages), however differs from operating system to operating system. Instructions can be found [here](https://github.com/ISI-MIP/isimip-qc/blob/main/README.md#prerequisites).
 
-If you work with different Python applications, we recommend to create a virtual enviroment for the protocol.
+If you work with different Python applications, we recommend to create a virtual environment for the protocol.
 
 ```bash
 # setup venv on Linux/macOS/Windows WSL

app/README.md

@@ -28,4 +28,4 @@ In order to rebuild the app or work on the code, the following setup needs to be
 
 5. Run `python3 build/assets.py --link` or `make dev` in the main protocol directory to link the assets instead of copying them.
 
-6. Before commiting any changes, run `npm run build:prod` or just `make` to create a production version of the app, which then will be part of the repository.
+6. Before committing any changes, run `npm run build:prod` or just `make` to create a production version of the app, which then will be part of the repository.

app/src/app.js

@@ -139,7 +139,7 @@ setTimeout(() => {
   })
 
   setTimeout(() => {
-    // scroll to anchor or position once everthing is settled
+    // scroll to anchor or position once everything is settled
     if (anchor) {
       anchor.scrollIntoView()
     }

app/src/components/badges/Sectors.js

@@ -7,7 +7,7 @@ const Sectors = ({ config, sectors }) => {
   if (sectors === undefined) {
     return <span className="badge badge-success badge-sector">all sectors</span>
   } else if (sectors === []) {
-    // by setting `sectors: []` the display of sectors can be ommited
+    // by setting `sectors: []` the display of sectors can be omitted
     return null
   } else if (sectors === null) {
     // for the title just display the configured sectors
@@ -17,7 +17,7 @@ const Sectors = ({ config, sectors }) => {
       return <span className="badge badge-success badge-sector">all sectors</span>
     }
   } else {
-    // some sectors are configured -> hightlight selected sectors
+    // some sectors are configured -> highlight selected sectors
     if (config.sectors !== undefined && config.sectors.length > 0) {
       // at least one sector is selected
       return sectors.map((sector, index) => {

build/protocol.py

@@ -63,8 +63,8 @@ def main():
     protocol_path = Path('protocol') / '00.base.md'
     template_string = protocol_path.read_text()
 
-    enviroment = Environment(loader=FileSystemLoader(['bibliography', 'protocol', 'templates']))
-    template = enviroment.from_string(template_string)
+    environment = Environment(loader=FileSystemLoader(['bibliography', 'protocol', 'templates']))
+    template = environment.from_string(template_string)
 
     md = template.render(commit_url=commit_url, commit_hash=commit_hash, commit_date=commit_date)
     html = markdown(md, extensions=[
@@ -84,10 +84,10 @@ def main():
     template_path = Path('templates') / 'layout.html'
     output_path = Path('output') / 'index.html'
     output_path.parent.mkdir(parents=True, exist_ok=True)
-    enviroment = Environment(loader=FileSystemLoader(['templates']))
+    environment = Environment(loader=FileSystemLoader(['templates']))
 
     with open(template_path, encoding='utf-8') as f:
-        template = enviroment.from_string(f.read())
+        template = environment.from_string(f.read())
 
     with open(output_path, 'w', encoding='utf-8') as f:
         f.write(template.render(html=html, definitions=json.dumps(definitions, indent=2), patterns=json.dumps(patterns, indent=2)))

definitions/climate_variable/lightning.yaml

@@ -23,7 +23,7 @@
   path: ISIMIP3b/InputData/climate/lightning/lightning_ukesm1-0-ll_<climate-scenario>_global_monthly_2010_2100.nc
   comment: >-
     Source: [Kaplan, Jed O., et al. 2023](https://doi.org/10.5281/zenodo.7511843).
-    This is the input data for the `varlightning` sensitivity experiments. Seperate
+    This is the input data for the `varlightning` sensitivity experiments. Separate
     datasets are available for ssp126, ssp370, and ssp585. Please note, as this dataset
     is produced using UKESM output, modelers should only use this data together with
     UKESM climate forcing.

definitions/geo_dataset.yaml

@@ -508,7 +508,7 @@
 
 - specifier: lake_elevation
   specifier_file: elevation
-  title: Lake Heigth
+  title: Lake Height
   group: lakes
   resolution: 0.5° grid
   path:

definitions/product.yaml

@@ -8,7 +8,7 @@
   title: Secondary Input Data
   description: >-
     Data that have been derived from or are related to the input data, but not described
-    in the simulation protocol (e.g. with a differnt spatial or temporal resolution).
+    in the simulation protocol (e.g. with a different spatial or temporal resolution).
 
 - specifier: OutputData
   title: Output Data

definitions/variable/peat.yaml

@@ -89,7 +89,7 @@
   - null
   - <pt>
   units: m
-  frequency: daily if possible, else montly
+  frequency: daily if possible, else monthly
   resolution: 0.5° grid
   comment: >-
     Water table level relative to the ground surface. Note that a negative value should
@@ -192,7 +192,7 @@
   - null
   - <pt>
   units: '1'
-  frequency: daily if possible, else montly
+  frequency: daily if possible, else monthly
   resolution: 0.5° grid
   comment: >-
     Grid fraction that is flooded, i.e. where the water table is above ground surface.

protocol/02.experiments.md

@@ -2,7 +2,7 @@
 
 In Table 2.1, we describe the different experiments for ISIMIP3. Each default experiment is defined by its **climate related forcing (CRF)** and the assumptions regarding **direct human forcing (DHF)**. The associated specifications all have a label such as `obsclim` or `histsoc` that are provided in Table 2.1 and further specified in Tables 2.2 and 2.3. These specifiers are used in the file names of the corresponding input files and should also be used for the names of the output files (see report model results [report model results](#5-reporting-model-results)). Sensitivity experiments are described as deviation from a default experiment and represented by labels that are used as a third specifier of the experiments. Their specific meanings are defined in Table 2.4.
 
-Please note that the experiments are different for ISIMIP3a and ISIMIP3b and some are sector specific. You can use the menu on the top-right of the page to select the sumulation round and sectors you are interested in.
+Please note that the experiments are different for ISIMIP3a and ISIMIP3b and some are sector specific. You can use the menu on the top-right of the page to select the simulation round and sectors you are interested in.
 
 ::: table identifier=experiments caption="Table 2.1: Experiment set-up. Each experiment is specified by the climate related forcing (top row) and the direct human forcing (bottom row). Sensitivity labels indicate deviations from the default settings.  Experiments are colored by group: group I (grey), group II (red) and group III (blue). The subtitles in the first row indicate how the experiment is defined in filenames."
 

protocol/04.output.md

@@ -83,7 +83,7 @@ Many variables are defined per area (unit m-2). Typically, and unless otherwise
 
     #### Information about soil organic carbon pools of different turnover times
 
-    Some variables can be provided seperately by soil organic carbon pools of different turnover times, if your model simulates those. This is done using the `-<pool>` extension. Please indicate them as `-fast`, `-slow`, and `-passive` and describe your definition of the turnover times in your model description. The extension is used in addition to the extension expressing the Plant Functional Type (PFT) and needs to put before it.
+    Some variables can be provided separately by soil organic carbon pools of different turnover times, if your model simulates those. This is done using the `-<pool>` extension. Please indicate them as `-fast`, `-slow`, and `-passive` and describe your definition of the turnover times in your model description. The extension is used in addition to the extension expressing the Plant Functional Type (PFT) and needs to put before it.
 
 ::: show sector=peat
 

requirements.txt

@@ -5,3 +5,4 @@ jsonschema
 markdown-customblocks
 pre-commit
 PyYAML
+typos