Implement CRAN feedback

.Rbuildignore

@@ -1,5 +1,7 @@
+^docs$
 ^\.github$
 ^pkgdown$
 ^_pkgdown\.yml$
 ^\.Rproj\.user$
 ^cran-comments\.md$
+^CRAN-SUBMISSION$

.gitignore

@@ -5,3 +5,4 @@ inst/doc
 vignettes/*.html
 vignettes/*.R
 docs/
+CRAN-SUBMISSION

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: enviPathR
-Title: The R client for the enviPath RESTful API
+Title: Client for the 'enviPath' RESTful API
 Version: 1.0.0
 Authors@R:
     c(person(given = "Giulio", family = "Benedetti",
           role = c("aut", "cre", "cph"),
           email = "giulio.benedetti@utu.fi",
           comment = c(ORCID = "0000-0002-8732-7692")))
 Description:
-    The environmental pathway database (enviPath) is a key resource for the
+    The environmental pathway database ('enviPath') is a key resource for the
     functional annotation and pathway prediction of microbial communities,
     providing knowledge on biotransformation pathways along with the chemical
     reactions and produced compounds. This package enables the programmatic

cran-comments.md

@@ -1,5 +1,5 @@
 ## R CMD check results
 
-0 errors ✔ | 0 warnings ✔ | 2 notes ✖
+0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
 * This is a new release.

tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json → tests/httptest/get/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json

@@ -9,11 +9,11 @@
     "educts": [
         {
             "compoundName": "4-Hydroxybutyraldehyde",
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d2c48ebe-5a5a-4f5b-b42e-8ff23c873f6c/structure/7281d994-9f4a-4f7f-9e50-90b131c11da3",
+            "id": "https://envipath.org/package_compound_structure/7281d994-9f4a-4f7f-9e50-90b131c11da3",
             "smiles": "C(CCO)C=O"
         }
     ],
-    "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a",
+    "id": "https://envipath.org/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a",
     "identifier": "reaction",
     "medlineRefs": [
 
@@ -22,7 +22,7 @@
     "name": "Eawag BBD reaction r0014",
     "pathways": [
         {
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3",
+            "id": "https://envipath.org/package_pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3",
             "name": "Tetrahydrofuran",
             "reviewStatus": "reviewed",
             "identifier": "pathway"
@@ -31,7 +31,7 @@
     "products": [
         {
             "compoundName": "4-Hydroxybutanoate",
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a41e6b76-b462-49d4-ae42-391ef00bf98c/structure/befe8eeb-e8f8-4b4a-90b1-d0584a75f8cb",
+            "id": "https://envipath.org/package_compound_structure/befe8eeb-e8f8-4b4a-90b1-d0584a75f8cb",
             "smiles": "C(CC(=O)[O-])CO"
         }
     ],

tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json → tests/httptest/link/package_compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json

@@ -11,7 +11,7 @@
             "06752"
         ]
     },
-    "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896",
+    "id": "https://envipath.org/package_compound/ec87b463-6a3c-4dfa-8b88-4637fc158896",
     "halflifes": [
 
     ],
@@ -23,7 +23,7 @@
     ],
     "pathways": [
         {
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232",
+            "id": "https://envipath.org/package_pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232",
             "name": "1,2-Dichloroethane",
             "reviewStatus": "reviewed",
             "identifier": "pathway"
@@ -34,7 +34,7 @@
     ],
     "reactions": [
         {
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a",
+            "id": "https://envipath.org/package_reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a",
             "name": "Eawag BBD reaction r0001",
             "reviewStatus": "reviewed",
             "identifier": "reaction"
@@ -46,7 +46,7 @@
     ],
     "structures": [
         {
-            "InChI": "InChI=1S/C2H4Cl2/c3-1-2-4/h1-2H2",
+            "InChI": "InChI=1S/C2H4Cl2_h1-2H2",
             "aliases": [
 
             ],
@@ -65,7 +65,7 @@
             "halflifes": [
 
             ],
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896/structure/7fa796ed-4816-4bc1-8c46-afdfd86ac8a3",
+            "id": "https://envipath.org/package_compound_structure/7fa796ed-4816-4bc1-8c46-afdfd86ac8a3",
             "identifier": "structure",
             "imageSize": 600,
             "inchikey": "WSLDOOZREJYCGB-UHFFFAOYSA-N",
@@ -74,7 +74,7 @@
             "name": "1,2-Dichloroethane",
             "pathways": [
                 {
-                    "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232",
+                    "id": "https://envipath.org/package_pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232",
                     "name": "1,2-Dichloroethane",
                     "reviewStatus": "reviewed",
                     "identifier": "pathway"
@@ -85,7 +85,7 @@
             ],
             "reactions": [
                 {
-                    "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a",
+                    "id": "https://envipath.org/package_reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a",
                     "name": "Eawag BBD reaction r0001",
                     "reviewStatus": "reviewed",
                     "identifier": "reaction"
@@ -98,7 +98,7 @@
             "smiles": "C(CCl)Cl"
         },
         {
-            "InChI": "InChI=1S/C2H4Cl2/c3-1-2-4/h1-2H2",
+            "InChI": "InChI=1S/C2H4Cl2_h1-2H2",
             "aliases": [
 
             ],
@@ -112,7 +112,7 @@
             "halflifes": [
 
             ],
-            "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896/structure/69d4e95c-30b9-43a3-b385-0f9ad853a79a",
+            "id": "https://envipath.org/package_compound_structure/69d4e95c-30b9-43a3-b385-0f9ad853a79a",
             "identifier": "structure",
             "imageSize": 600,
             "inchikey": "WSLDOOZREJYCGB-UHFFFAOYSA-N",