Fix linting issues (#97)

* Fix file write issue in PrepareJobFile function

* linting

* update gitignore

.github/dependabot.yml

@@ -5,7 +5,7 @@
 
 version: 2
 updates:
-  - package-ecosystem: "gomod" # See documentation for possible values
-    directory: "/" # Location of package manifests
+  - package-ecosystem: gomod # See documentation for possible values
+    directory: / # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: weekly

.github/workflows/lint.yml

@@ -2,6 +2,8 @@ name: linting
 
 on: push
 
+permissions: read-all
+
 jobs:
   linting:
     runs-on: ubuntu-latest

.github/workflows/unittests.yml

@@ -5,6 +5,8 @@ env:
 
 on: push
 
+permissions: read-all
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -17,7 +19,7 @@ jobs:
     steps:
       - uses: actions/setup-go@v3
         with:
-          go-version: "^1.19"
+          go-version: ^1.21
       - uses: actions/checkout@v2
 
       - name: Install dependencies

.gitignore

@@ -1,4 +1,3 @@
-
 #***********************************************************************
 # VSCode things
 .vscode
@@ -10,3 +9,4 @@ example/**/run*
 bm-goes-here/
 dev/
 #***********************************************************************
+haddockrunner

.howfairis.yml

@@ -4,6 +4,6 @@
 #skip_license_checks_reason: <reason for skipping goes here>
 #skip_registry_checks_reason: <reason for skipping goes here>
 #skip_citation_checks_reason: <reason for skipping goes here>
-skip_checklist_checks_reason: "I'm using the Codacy dashboard to guide my development"
+skip_checklist_checks_reason: I'm using the Codacy dashboard to guide my development
 
 ignore_commented_badges: false

.trunk/trunk.yaml

@@ -17,9 +17,12 @@ runtimes:
     - [email protected]
 # This is the section where you manage your linters. (https://docs.trunk.io/check/configuration)
 lint:
+  disabled:
+    - terrascan
+    - trivy
+    - checkov
   enabled:
     - [email protected]
-    - [email protected]
     - git-diff-check
     - [email protected]
     - [email protected]
@@ -29,9 +32,7 @@ lint:
     - [email protected]
     - [email protected]
     - [email protected]
-    - [email protected]
-    - [email protected]
-    - [email protected]
+    - [email protected]
     - [email protected]
 actions:
   enabled:

example/haddock24.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #===============================================================================
-HADDOCK24_DIR="$HOME/repos/haddock24"
+HADDOCK24_DIR="${HOME}/repos/haddock24"
 
 ### Activate the virtual environment
 ## if your haddock24 installation uses venv
@@ -9,13 +9,13 @@ HADDOCK24_DIR="$HOME/repos/haddock24"
 conda activate haddock24
 
 ### Set the environment variables
-export HADDOCK="$HADDOCK24_DIR"
-export HADDOCKTOOLS="$HADDOCK/tools"
-export PYTHONPATH="${PYTHONPATH}:$HADDOCK"
+export HADDOCK="${HADDOCK24_DIR}"
+export HADDOCKTOOLS="${HADDOCK}/tools"
+export PYTHONPATH="${PYTHONPATH}:${HADDOCK}"
 
 #######################################################################
 # IMPORTANT: HADDOCK2.4 might fail with exit code 0 even if it fails
 #######################################################################
 
-python "$HADDOCK/Haddock/RunHaddock.py"
+python "${HADDOCK}/Haddock/RunHaddock.py"
 #===============================================================================

example/haddock3.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 #===============================================================================
 
+# shellcheck source=/dev/null
 source /opt/conda/etc/profile.d/conda.sh
 conda activate env
 

go.mod

@@ -1,10 +1,10 @@
 module haddockrunner
 
-go 1.19
+go 1.21
 
 require (
 	github.com/go-test/deep v1.1.0
 	github.com/golang/glog v1.2.0
 	golang.org/x/text v0.14.0
 	gopkg.in/yaml.v3 v3.0.1
-)
+)

go.sum

@@ -1,11 +1,27 @@
+github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
+github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/go-test/deep v1.1.0 h1:WOcxcdHcvdgThNXjw0t76K42FXTU7HpNQWHpA2HHNlg=
 github.com/go-test/deep v1.1.0/go.mod h1:5C2ZWiW0ErCdrYzpqxLbTX7MG14M9iiw8DgHncVwcsE=
 github.com/golang/glog v1.2.0 h1:uCdmnmatrKCgMBlM4rMuJZWOkPDqdbZPnrMXDY4gI68=
 github.com/golang/glog v1.2.0/go.mod h1:6AhwSGph0fcJtXVM/PEHPqZlFeoLxhs7/t5UDAwmO+w=
+github.com/golangci/dupl v0.0.0-20180902072040-3e9179ac440a h1:w8hkcTqaFpzKqonE9uMCefW1WDie15eSP/4MssdenaM=
+github.com/golangci/dupl v0.0.0-20180902072040-3e9179ac440a/go.mod h1:ryS0uhF+x9jgbj/N71xsEqODy9BN81/GonCZiOzirOk=
 github.com/google/go-cmp v0.6.0 h1:ofyhxvXcZhMsU5ulbFiLKl/XBFqE1GSq7atu8tAmTRI=
+github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
+github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
+github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/stretchr/objx v0.4.0/go.mod h1:YvHI0jy2hoMjB+UWwv71VJQ9isScKT/TqJzVSSt89Yw=
+github.com/stretchr/objx v0.5.0 h1:1zr/of2m5FGMsad5YfcqgdqdWrIhu+EBEJRhR1U7z/c=
+github.com/stretchr/objx v0.5.0/go.mod h1:Yh+to48EsGEfYuaHDzXPcE3xhTkx73EhmCGUpEOglKo=
+github.com/stretchr/testify v1.7.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
+github.com/stretchr/testify v1.8.0/go.mod h1:yNjHg4UonilssWZ8iaSj1OCr/vHnekPRkoO+kdMU+MU=
+github.com/stretchr/testify v1.8.4 h1:CcVxjf3Q8PM0mHUKJCdn+eZZtm5yQwehR5yeSVQQcUk=
+github.com/stretchr/testify v1.8.4/go.mod h1:sz/lmYIOXD/1dqDmKjjqLyZ2RngseejIcXlSw2iwfAo=
 golang.org/x/text v0.14.0 h1:ScX5w1eTa3QqT8oi6+ziP7dTV1S2+ALU0bI+0zXKWiQ=
 golang.org/x/text v0.14.0/go.mod h1:18ZOQIKpY8NJVqYksKHtTdi31H5itFRjB5/qKTNYzSU=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
 gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=

runner/jobs.go

@@ -200,7 +200,7 @@ func (j *Job) PrepareJobFile(executable string) error {
 	}
 
 	// Write the JobFile
-	f.WriteString(header + body)
+	_, _ = f.WriteString(header + body)
 
 	_ = f.Close()