2024 Update #20

stopfstedt · 2024-02-10T01:30:20Z

PHPUnit 11 requires PHP 8.1 or higher.

staying in lock-step with required min version specified in package file.

we're specifying everything we need in the new phpcs config file now.

- declare PHP strict mode - resolves all PHPUnit-related deprecations - resolves all Faker-related deprecations

- strict mode - type hints - ditch pointless comments

according to the DTD, ConceptRelation::RelationName is an "implied" attribute, which makes it optional.

meld it into Reference class, its only consumer.

…cks. this will come in handy when testing Models with nullable attrs.

*headdesk

- add type hints where missing - simplify paths via imports - An vs a - drop unnecessary function args where defaults suffice - fix up code comments

courtesy of PHPStan lvl 5. explanation: that local variable was never instantiated as a Reference object, thus remaining NULL throughout parsing, thus the if conditional was always evaluating to FALSE. turns out that we don't need to local Referencevariable after all - we want to set concept id (UI) and name directly on the Concept object. which we've been doing. in sum - not a bugfix, just cleanup.

exclude the vendor dir. in the CI, lint all configured dirs in one step.

…butes.

copied and stripped down from ilios/ilios.

stopfstedt · 2024-02-13T23:18:32Z

stefan@nichtsnutz: ~/dev/projects/mesh-parser on update_2024
$ php -dxdebug.mode=coverage bin/phpunit --coverage-text
PHPUnit 11.0.3 by Sebastian Bergmann and contributors.

Runtime:       PHP 8.3.2-1+ubuntu22.04.1+deb.sury.org+1 with Xdebug 3.3.1
Configuration: /home/stefan/dev/projects/mesh-parser/phpunit.xml

................................................................. 65 / 65 (100%)


Time: 00:00.254, Memory: 14.00 MB

OK (65 tests, 427 assertions)

Generating code coverage report in HTML format ... done [00:00.065]


Code Coverage Report:       
  2024-02-13 23:17:43       
                            
 Summary:                   
  Classes: 100.00% (10/10)  
  Methods: 100.00% (105/105)
  Lines:   100.00% (331/331)

Ilios\MeSH\Model\AllowableQualifier
  Methods: 100.00% ( 4/ 4)   Lines: 100.00% (  4/  4)
Ilios\MeSH\Model\Concept
  Methods: 100.00% (18/18)   Lines: 100.00% ( 18/ 18)
Ilios\MeSH\Model\ConceptRelation
  Methods: 100.00% ( 6/ 6)   Lines: 100.00% (  6/  6)
Ilios\MeSH\Model\Descriptor
  Methods: 100.00% (34/34)   Lines: 100.00% ( 34/ 34)
Ilios\MeSH\Model\DescriptorSet
  Methods: 100.00% ( 6/ 6)   Lines: 100.00% (  8/  8)
Ilios\MeSH\Model\EntryCombination
  Methods: 100.00% ( 8/ 8)   Lines: 100.00% (  8/  8)
Ilios\MeSH\Model\Identifiable
  Methods: 100.00% ( 2/ 2)   Lines: 100.00% (  2/  2)
Ilios\MeSH\Model\Reference
  Methods: 100.00% ( 2/ 2)   Lines: 100.00% (  2/  2)
Ilios\MeSH\Model\Term
  Methods: 100.00% (20/20)   Lines: 100.00% ( 20/ 20)
Ilios\MeSH\Parser
  Methods: 100.00% ( 5/ 5)   Lines: 100.00% (229/229)

jrjohnson · 2024-02-13T23:32:44Z

.github/dependabot.yml

+  - package-ecosystem: composer
+    directory: "/"
+    schedule:
+      interval: daily


Given our infrequent release here I think weekly may be a better choice with less PRs to manage. I wonder if it's worth pulling in the update-dependencies and maybe adding auto merge as well to keep the number even lower?

changed to weekly and deps update workflow added ✔️

jrjohnson · 2024-02-13T23:33:41Z

composer.json

@@ -6,7 +6,7 @@
    "Ilios",
    "MeSH"
  ],
-  "homepage": "http://iliosproject.org/",
+  "homepage": "https://iliosproject.org/",


jrjohnson · 2024-02-13T23:38:55Z

src/Ilios/MeSH/Parser.php

-    const TREE_NUMBER = 'TreeNumber';
-    const TREE_NUMBER_LIST = 'TreeNumberList';
-    const YEAR = 'Year';
+    public const ABBREVIATION = 'Abbreviation';


I don't know that it matters, but are these public? I searched for a few of them and they seem to only be used in this class.

PHPCS won't have it any other way. without an accessor, it will emit this warning:

Visibility must be declared on all constants if your project supports PHP 7.1 or later

I was assuming we'd go protected instead, but let's make that a next time problem.

this is a lateral shift, as these are public by default/without the accessor. don't see why not, the values can't be tampered with.

jrjohnson · 2024-02-13T23:42:15Z

tests/Ilios/MeSH/Model/BaseTestCase.php

+    }
+
+    /**
+     * @param  string $property


docblocks in this file are duplicates of declarations in the code. Just remove them?

done. ✔️

jrjohnson · 2024-02-13T23:43:38Z

tests/Ilios/MeSH/desc.xml

@@ -135,6 +135,8 @@ It contains all possible elements defined by the schema.
                <CASN1Name>a casn1 name</CASN1Name>
                <RegistryNumber>00000AAAAA</RegistryNumber>
                <ScopeNote>a scope note</ScopeNote>
+                <TranslatorsEnglishScopeNote>something in English.</TranslatorsEnglishScopeNote>
+                <TranslatorsScopeNote>i got nothing</TranslatorsScopeNote>


zero points for creativity!

straight outta Ilios

stopfstedt force-pushed the update_2024 branch 3 times, most recently from 0474e52 to 5fd8fdb Compare February 12, 2024 20:46

stopfstedt added 14 commits February 12, 2024 15:30

updates dependencies.

799ee7e

tranform phpunit config file to v11 compliant format.

335aa1d

adjust name of phpunit cache file in git ignore list.

04b6ccf

update minimum PHP version requirement to 8.1

e5a48af

PHPUnit 11 requires PHP 8.1 or higher.

bump PHP version to 8.1 on GH actions.

845d813

staying in lock-step with required min version specified in package file.

adds phpcs config file and configures its cache file to be git-ignored.

88cf6db

ditch command line flags from phpcs invocations in the CI.

05e8110

we're specifying everything we need in the new phpcs config file now.

updates test coverage.

d611111

- declare PHP strict mode - resolves all PHPUnit-related deprecations - resolves all Faker-related deprecations

updates model classes.

87eb375

- strict mode - type hints - ditch pointless comments

make $name attr "nullable".

b1d7776

according to the DTD, ConceptRelation::RelationName is an "implied" attribute, which makes it optional.

dissolve Nameable trait.

e9d89d5

meld it into Reference class, its only consumer.

expand scope of setter/getter test helper to allow for NULL input che…

6da2d64

…cks. this will come in handy when testing Models with nullable attrs.

unearth PHPUnit attribute from docblock.

eebef5a

*headdesk

appease the code linter.

871576c

stopfstedt force-pushed the update_2024 branch from 5fd8fdb to 7f45b20 Compare February 12, 2024 23:30

updates links and docs.

8c1d34c

stopfstedt force-pushed the update_2024 branch from 7f45b20 to 8c1d34c Compare February 12, 2024 23:36

stopfstedt added 10 commits February 12, 2024 15:41

expand test matrix to PHP 8.2 and 8.3

583c3f4

ditch PHP 8.1. update dependencies.

d15f0ab

https it is.

c590765

add PHPStan to the mix.

573650f

declare the XMLWriter PHP extension as requirement.

8aeddfc

declare the DOM PHP extension as requirement.

9407b30

cleanup the Parser class.

4d019ca

- add type hints where missing - simplify paths via imports - An vs a - drop unnecessary function args where defaults suffice - fix up code comments

rm unused class constants.

7449a01

consolidate case statements with same body.

510c548

stopfstedt added 8 commits February 12, 2024 16:53

update file name in code example.

d7c4b57

dial in PHPCS config and streamline linting step in the CI.

0a32f40

exclude the vendor dir. in the CI, lint all configured dirs in one step.

run PHPStan in the CI pipeline.

8774940

update actions/checkout to v4

638ae89

initalize nullable class member to null.

66418e5

updates model tests to invoke getter/setters tests for nullable attri…

d07af88

…butes.

configure PHPUnit for code coverage.

f4f66aa

update setter/getter test helper for object attrs that can be nulled.

97885ce

stopfstedt force-pushed the update_2024 branch from ee86838 to 97885ce Compare February 13, 2024 17:33

stopfstedt added 3 commits February 13, 2024 09:50

adds dependabot configuration.

d2f01a5

copied and stripped down from ilios/ilios.

git ignore phpunit.xml file.

6ce9da8

put all remaining model attrs under test coverage.

351eec9

stopfstedt marked this pull request as ready for review February 13, 2024 23:18

stopfstedt requested a review from jrjohnson February 13, 2024 23:18

stopfstedt assigned jrjohnson Feb 13, 2024

jrjohnson requested changes Feb 13, 2024

View reviewed changes

stopfstedt added 3 commits February 13, 2024 15:49

change dependabot interval from daily to weekly.

b33920c

adds dependency update workflow.

dbd97cd

straight outta Ilios

rm pointless docblocks.

05b99a6

stopfstedt requested a review from jrjohnson February 14, 2024 00:01

jrjohnson approved these changes Feb 14, 2024

View reviewed changes

jrjohnson merged commit 051a015 into ilios:master Feb 14, 2024
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2024 Update #20

2024 Update #20

stopfstedt commented Feb 10, 2024 •

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stopfstedt commented Feb 13, 2024

jrjohnson Feb 13, 2024

stopfstedt Feb 13, 2024

jrjohnson Feb 13, 2024

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2024 Update #20

2024 Update #20

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stopfstedt commented Feb 10, 2024 •

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stopfstedt Feb 13, 2024 •

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