Code cleanup and better string handling (#20)

Primarily a housekeeping release. Took care of some minor linting and some redundant code. Made some changes to how string were being handled for various input. The allocation should be more efficient and safer as a result. Could see some minor impact on speed as a couple loops were added to calculate string length. Overall should improve ability to maintain and debug the code. Added GitHub actions for CI. This will close #19. Needed to add a conditional compile for strlcat since some systems (such as OSX) have it natively.
nawendt · Sep 16, 2022 · 226f2ae · 226f2ae
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,9 +3,12 @@
 ^README\.md$
 ^\.DS_Store$
 ^\.Rhistory$
+^\.git$
+^\.github$
 ^\.git_commit_template$
 ^\.gitignore$
 ^\.travis\.yml$
+^\.vscode$
 ^m4$
 ^install_.*\.sh$
 ^appveyor\.yml$

diff --git a/.github/workflows/check-latest.yaml b/.github/workflows/check-latest.yaml
@@ -0,0 +1,63 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: Build (Latest ecCodes)
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      ECCODES_VERSION: 2.27.0
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libproj-dev libaec-dev libopenjp2-7-dev libpng-dev
+      
+      - name: Install macOS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install proj libaec openjpeg zlib
+
+      - name: Build eccodes from source
+        run: ./install_eccodes.sh
+        shell: bash          
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/check-minimum.yaml b/.github/workflows/check-minimum.yaml
@@ -0,0 +1,71 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: Build (Minimum ecCodes)
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      ECCODES_VERSION: 2.19.0
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libproj-dev libaec-dev libopenjp2-7-dev libpng-dev
+      
+      - name: Install macOS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install proj libaec openjpeg zlib
+
+      - name: Build eccodes from source (Linux)
+        if: runner.os == 'Linux'
+        run: ./install_eccodes.sh
+        shell: bash   
+
+      - name: Build eccodes from source (macOS)
+        if: runner.os == 'macOS'
+        env:
+          OPENJPEG_INCLUDE_DIR: /usr/local/include/openjpeg-2.5
+        run: ./install_eccodes.sh
+        shell: bash          
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: Build (System ecCodes)
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libproj-dev libeccodes-dev
+      
+      - name: Install macOS dependencies
+        if: runner.os == 'macOS'
+        run: brew install proj eccodes
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -0,0 +1,35 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: Lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install gribr dependencies
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libproj-dev libeccodes-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,36 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: Codecov
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install gribr dependencies
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libproj-dev libeccodes-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,7 @@
 autom4te.cache
 *.log
 *.status
+.vscode
 src/*.o
 src/*.so
 src/*.dll

diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,14 @@
 Package: gribr
 Type: Package
 Title: Read GRIB Files
-Version: 1.2.3
-Date: 2021-01-14
+Version: 1.2.4
+Date: 2022-09-16
 Author: Nathan Wendt <[email protected]>
 Maintainer: Nathan Wendt <[email protected]>
 BugReports: https://github.com/nawendt/gribr/issues
 Description: R interface for GRIB files using ECMWF ecCodes. Easily read GRIB data into native R data types.
-License: BSD_2_clause + file LICENSE
-LazyData: TRUE
-RoxygenNote: 7.1.1
+License: BSD_3_clause + file LICENSE
+RoxygenNote: 7.2.1
 Encoding: UTF-8
 NeedsCompilation: yes
 SystemRequirements: ECMWF ecCodes (>= 2.19.0)

diff --git a/LICENSE b/LICENSE
@@ -1,15 +1,21 @@
-Copyright (c) 2016, Nathan Wendt
+BSD 3-Clause License
+
+Copyright (c) 2022, Nathan Wendt
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
 
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,grib)
+export(grib_api_version)
 export(grib_close)
 export(grib_cube)
 export(grib_expand_grids)