ci!: 1.10 (lts) minimum version + complete CI

Author: cvigilv

.github/workflows/CI.yml

@@ -6,19 +6,31 @@ on:
     tags: ['*']
   pull_request:
 concurrency:
-  # Skip intermediate builds: always.
-  # Cancel intermediate builds: only if it is a pull request build.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
+  format:
+    name: Code formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v1
+      - name: Install Runic
+        run: julia -e 'using Pkg; Pkg.add("Runic")'
+      - name: Check formatting
+        run: julia -e 'using Runic; Runic.main(["--check", "src/", "test/", "docs/"])'
+
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Test (${{ matrix.version }}; ${{ matrix.os }} ${{ matrix.arch }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.9'
+          - '1.10'
           - 'nightly'
         os:
           - ubuntu-latest
@@ -33,8 +45,11 @@ jobs:
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        timeout-minutes: 10
       - uses: julia-actions/julia-processcoverage@v1
+        if: matrix.version == '1.10' && matrix.os == 'ubuntu-latest'
       - uses: codecov/codecov-action@v3
+        if: matrix.version == '1.10' && matrix.os == 'ubuntu-latest'
         with:
           files: lcov.info
   docs:

Project.toml

@@ -1,17 +1,18 @@
 name = "KEGGAPI"
 uuid = "e8256861-d17c-4800-bf17-838497555b93"
-authors = ["Nicholas Geoffrion", "Maria Victoria Aguilar Pontes"]
 version = "1.0.0-DEV"
+authors = ["Nicholas Geoffrion", "Maria Victoria Aguilar Pontes", "Carlos Vigil-Vásquez"]
 
 [deps]
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 
 [compat]
 HTTP = "1"
-julia = "1"
+julia = "1.10"
 
 [extras]
+Runic = "62bfec6d-59d7-401d-8490-b29ee721c001"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Runic"]

README.md

@@ -1,9 +1,9 @@
 ![plot](./assets/logo/keggapi-logo.jpg)
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://bwbioinfo.github.io/KEGGAPI.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://bwbioinfo.github.io/KEGGAPI.jl/dev/)
-[![Build Status](https://github.com/bwbioinfo/KEGGAPI.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/bwbioinfo/KEGGAPI.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/bwbioinfo/KEGGAPI.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/bwbioinfo/KEGGAPI.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cvigilv.github.io/KEGGAPI.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cvigilv.github.io/KEGGAPI.jl/dev/)
+[![Build Status](https://github.com/cvigilv/KEGGAPI.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/cvigilv/KEGGAPI.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/cvigilv/KEGGAPI.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/cvigilv/KEGGAPI.jl)
 
 
 KEGGAPI.jl is a Julia package for accesing the Kyoto Encyclopedia of Genes and Genomes, striving to take advantage of the speed and flexibility that Julia offers and make it accessible to the bioinformatics and functional annotation communities.

docs/make.jl

@@ -1,20 +1,20 @@
 using KEGGAPI
 using Documenter
 
-DocMeta.setdocmeta!(KEGGAPI, :DocTestSetup, :(using KEGGAPI); recursive=true)
+DocMeta.setdocmeta!(KEGGAPI, :DocTestSetup, :(using KEGGAPI); recursive = true)
 
 makedocs(;
-    modules=[KEGGAPI],
-    authors="Nicholas Geoffrion, Maria Victoria Aguilar Pontes",
-    repo="https://github.com/bwbioinfo/KEGGAPI.jl/blob/{commit}{path}#{line}",
-    sitename="KEGGAPI.jl",
-    format=Documenter.HTML(;
-        prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://bwbioinfo.github.io/KEGGAPI.jl",
-        edit_link="main",
-        assets=String[],
+    modules = [KEGGAPI],
+    authors = "Nicholas Geoffrion, Maria Victoria Aguilar Pontes, Carlos Vigil-Vásquez",
+    repo = "https://github.com/cvigilv/KEGGAPI.jl/blob/{commit}{path}#{line}",
+    sitename = "KEGGAPI.jl",
+    format = Documenter.HTML(;
+        prettyurls = get(ENV, "CI", "false") == "true",
+        canonical = "https://cvigilv.github.io/KEGGAPI.jl",
+        edit_link = "main",
+        assets = String[],
     ),
-    pages=[
+    pages = [
         "Home" => "index.md",
         "Manual" => Any[
             "Guide" => "man/guide.md",
@@ -26,6 +26,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/bwbioinfo/KEGGAPI.jl",
-    devbranch="main",
+    repo = "github.com/cvigilv/KEGGAPI.jl",
+    devbranch = "main",
 )

examples/example01.jl

@@ -73,4 +73,4 @@ kegg_link = KEGGAPI.link("pathway", "dr");
 ## Get an image
 kegg_image = KEGGAPI.get_image("hsa00010");
 ## Save an image
-KEGGAPI.save_image(kegg_image, "image.png");
+KEGGAPI.save_image(kegg_image, "image.png");

src/Conv.jl

@@ -1,4 +1,3 @@
-
 """
 KEGGAPI.conv(<target_db>, <source_db>)
 
@@ -19,12 +18,11 @@ function conv(target_db::String, source_db::String)
     # Define the URL for the API request.
     url = "https://rest.kegg.jp/conv/$target_db/$source_db"
     response_text = request(url)
-    kegg_data = 
+    kegg_data =
         conv_parser(
-            response_text, 
-            url
-            )
-    # return the arrays 
+        response_text,
+        url
+    )
+    # return the arrays
     return kegg_data
 end
-

src/Find.jl

@@ -1,4 +1,3 @@
-
 """
 KEGGAPI.find(database, query) -> KeggTupleList
 
@@ -10,10 +9,10 @@ KEGGAPI.find("compound","glucose")
 ```
 """
 function find(database::String, query::String, option::String = "")
-# This function retrieves a list of entries from a specific database from the KEGG API.
+    # This function retrieves a list of entries from a specific database from the KEGG API.
     query = replace(query, " " => "+")
     # Check if the requested database is a "pathway" database
-    if database in ["pathway","genes", "module", "orthology", "disease", "brite"]
+    if database in ["pathway", "genes", "module", "orthology", "disease", "brite"]
         if option != ""
             throw(ArgumentError("The option argument is not available for pathway and genes databases"))
         end
@@ -34,7 +33,7 @@ function find(database::String, query::String, option::String = "")
         # If the database is not a pathway database, print a message indicating that the requested list is not available
         print("The find route you are looking for is not available")
         # Return an empty array
-        kegg_data = [] 
+        kegg_data = []
     end
     # Return the parsed data or an empty array if not available
     return kegg_data

src/Get.jl

@@ -1,4 +1,3 @@
-
 """
 KEGGAPI.get(query, option) -> Vector
 
@@ -25,18 +24,18 @@ first(kegg_get_compounds)
 """
 function kegg_get(query::Vector{String}, option::String = "")
     # This function retrieves a list of entries from a specific database from the KEGG API.
-    
+
     # Set the chunk size for processing multiple elements in each request
     chunk_size = 10
-    
+
     # Calculate the number of chunks needed to process all elements in the query
     query_elements = length(query)
     query_chunks = ceil(Int, query_elements / chunk_size)
-    
+
     # Initialize arrays to store URLs and retrieved data
     urls = String[]
     data = String[]
-    
+
     # Check if the option is "aaseq" or "ntseq"
     if option == "aaseq" || option == "ntseq"
         # If there are more than 10 queries, process in chunks
@@ -45,28 +44,28 @@ function kegg_get(query::Vector{String}, option::String = "")
                 # Calculate start and end indices for the current chunk
                 start_index = (i - 1) * chunk_size + 1
                 end_index = min(i * chunk_size, query_elements)
-                
+
                 # Extract the current chunk of queries
                 chunk = query[start_index:end_index]
-                
+
                 # Join the queries with "+" for URL construction
                 chunk_query = join(chunk, "+")
-                
+
                 # Construct the URL for the API request
                 url = "https://rest.kegg.jp/get/$chunk_query/$option"
-                
+
                 # Store the URL for reference
                 push!(urls, url)
-                
+
                 # Request data from the URL
                 response_text = request(url)
-                
+
                 # Process the response and extract data
                 for datum in split(response_text, r"(\n>|^>)")[2:end]
                     datum = replace(datum, r"\n$" => "")
-                    push!(data, ">"*datum)
+                    push!(data, ">" * datum)
                 end
-                
+
                 # Introduce a delay before the next request
                 sleep(0.1)
             end
@@ -78,7 +77,7 @@ function kegg_get(query::Vector{String}, option::String = "")
             push!(urls, url)
             for datum in split(response_text, r"(\n>|^>)")[2:end]
                 datum = replace(datum, r"\n$" => "")
-                push!(data, ">"*datum)
+                push!(data, ">" * datum)
             end
         end
     else
@@ -88,28 +87,28 @@ function kegg_get(query::Vector{String}, option::String = "")
                 # Calculate start and end indices for the current chunk
                 start_index = (i - 1) * chunk_size + 1
                 end_index = min(i * chunk_size, query_elements)
-                
+
                 # Extract the current chunk of queries
                 chunk = query[start_index:end_index]
-                
+
                 # Join the queries with "+" for URL construction
                 chunk_query = join(chunk, "+")
-                
+
                 # Construct the URL for the API request
                 url = "https://rest.kegg.jp/get/$chunk_query/$option"
-                
+
                 # Store the URL for reference
                 push!(urls, url)
-                
+
                 # Request data from the URL
                 response_text = request(url)
-                
+
                 # Process the response and extract data
                 response_text2 = replace(response_text, r"\n///([^/]*)$" => "")
                 for datum in split(response_text2, "\n///\n")
                     push!(data, datum)
                 end
-                
+
                 # Introduce a delay before the next request
                 sleep(0.1)
             end
@@ -125,10 +124,10 @@ function kegg_get(query::Vector{String}, option::String = "")
             end
         end
     end
-    
+
     # Combine URLs and data into a single array
     kegg_data = [urls, data]
-    
+
     # Return the parsed data or an empty array if not available
     return kegg_data
 end

src/Images.jl

@@ -32,4 +32,4 @@ function save_image(image::Vector, filename::String)
         write(f, image)
     end
     return filename
-end
+end

src/Info.jl

@@ -17,4 +17,4 @@ function info(database::String)
     response_text = request(url)
     # Return the lines as a string.
     return response_text
-end
+end