diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 0efc119..7d520f5 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,10 +1,8 @@ on: push: - branches: - - master + branches: [main, master] pull_request: - branches: - - master + branches: [main, master] name: test-coverage @@ -14,24 +12,58 @@ permissions: jobs: test-coverage: - runs-on: macOS-latest + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: - r-version: 'release' + use-public-rspm: true - - name: Install dependencies + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Install package dependencies run: | install.packages("pak") pak::pkg_install(".", dependencies = TRUE) - pak::pkg_install("covr") shell: Rscript {0} - name: Test coverage - run: covr::codecov() + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + print(cov) + covr::to_cobertura(cov) shell: Rscript {0} - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + + - uses: codecov/codecov-action@v5 + with: + # Fail if error if not on PR, or if on PR and token is given + fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} + files: ./cobertura.xml + plugins: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/DESCRIPTION b/DESCRIPTION index 5528a23..f2e8c42 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: tailor Type: Package Title: Tool for Adapter-domain Identification and Linking Of RBPs -Version: 0.1.0 +Version: 0.1.1 Authors@R: c( person("András", "Asbóth", role = c("aut", "cre"), email = "sbthandras+bioinfo@gmail.com", @@ -29,6 +29,8 @@ Imports: reshape2, tibble, tidyr +Suggests: + testthat Remotes: stitam/breakpoint License: GPL (>= 3) diff --git a/LICENSE b/LICENSE deleted file mode 100644 index f288702..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/LICENSE.md b/LICENSE.md deleted file mode 100644 index 175443c..0000000 --- a/LICENSE.md +++ /dev/null @@ -1,595 +0,0 @@ -GNU General Public License -========================== - -_Version 3, 29 June 2007_ -_Copyright © 2007 Free Software Foundation, Inc. <>_ - -Everyone is permitted to copy and distribute verbatim copies of this license -document, but changing it is not allowed. - -## Preamble - -The GNU General Public License is a free, copyleft license for software and other -kinds of works. - -The licenses for most software and other practical works are designed to take away -your freedom to share and change the works. By contrast, the GNU General Public -License is intended to guarantee your freedom to share and change all versions of a -program--to make sure it remains free software for all its users. We, the Free -Software Foundation, use the GNU General Public License for most of our software; it -applies also to any other work released this way by its authors. You can apply it to -your programs, too. - -When we speak of free software, we are referring to freedom, not price. Our General -Public Licenses are designed to make sure that you have the freedom to distribute -copies of free software (and charge for them if you wish), that you receive source -code or can get it if you want it, that you can change the software or use pieces of -it in new free programs, and that you know you can do these things. - -To protect your rights, we need to prevent others from denying you these rights or -asking you to surrender the rights. Therefore, you have certain responsibilities if -you distribute copies of the software, or if you modify it: responsibilities to -respect the freedom of others. - -For example, if you distribute copies of such a program, whether gratis or for a fee, -you must pass on to the recipients the same freedoms that you received. You must make -sure that they, too, receive or can get the source code. And you must show them these -terms so they know their rights. - -Developers that use the GNU GPL protect your rights with two steps: **(1)** assert -copyright on the software, and **(2)** offer you this License giving you legal permission -to copy, distribute and/or modify it. - -For the developers' and authors' protection, the GPL clearly explains that there is -no warranty for this free software. For both users' and authors' sake, the GPL -requires that modified versions be marked as changed, so that their problems will not -be attributed erroneously to authors of previous versions. - -Some devices are designed to deny users access to install or run modified versions of -the software inside them, although the manufacturer can do so. This is fundamentally -incompatible with the aim of protecting users' freedom to change the software. The -systematic pattern of such abuse occurs in the area of products for individuals to -use, which is precisely where it is most unacceptable. Therefore, we have designed -this version of the GPL to prohibit the practice for those products. If such problems -arise substantially in other domains, we stand ready to extend this provision to -those domains in future versions of the GPL, as needed to protect the freedom of -users. - -Finally, every program is threatened constantly by software patents. States should -not allow patents to restrict development and use of software on general-purpose -computers, but in those that do, we wish to avoid the special danger that patents -applied to a free program could make it effectively proprietary. To prevent this, the -GPL assures that patents cannot be used to render the program non-free. - -The precise terms and conditions for copying, distribution and modification follow. - -## TERMS AND CONDITIONS - -### 0. Definitions - -“This License” refers to version 3 of the GNU General Public License. - -“Copyright” also means copyright-like laws that apply to other kinds of -works, such as semiconductor masks. - -“The Program” refers to any copyrightable work licensed under this -License. Each licensee is addressed as “you”. “Licensees” and -“recipients” may be individuals or organizations. - -To “modify” a work means to copy from or adapt all or part of the work in -a fashion requiring copyright permission, other than the making of an exact copy. The -resulting work is called a “modified version” of the earlier work or a -work “based on” the earlier work. - -A “covered work” means either the unmodified Program or a work based on -the Program. - -To “propagate” a work means to do anything with it that, without -permission, would make you directly or secondarily liable for infringement under -applicable copyright law, except executing it on a computer or modifying a private -copy. Propagation includes copying, distribution (with or without modification), -making available to the public, and in some countries other activities as well. - -To “convey” a work means any kind of propagation that enables other -parties to make or receive copies. Mere interaction with a user through a computer -network, with no transfer of a copy, is not conveying. - -An interactive user interface displays “Appropriate Legal Notices” to the -extent that it includes a convenient and prominently visible feature that **(1)** -displays an appropriate copyright notice, and **(2)** tells the user that there is no -warranty for the work (except to the extent that warranties are provided), that -licensees may convey the work under this License, and how to view a copy of this -License. If the interface presents a list of user commands or options, such as a -menu, a prominent item in the list meets this criterion. - -### 1. Source Code - -The “source code” for a work means the preferred form of the work for -making modifications to it. “Object code” means any non-source form of a -work. - -A “Standard Interface” means an interface that either is an official -standard defined by a recognized standards body, or, in the case of interfaces -specified for a particular programming language, one that is widely used among -developers working in that language. - -The “System Libraries” of an executable work include anything, other than -the work as a whole, that **(a)** is included in the normal form of packaging a Major -Component, but which is not part of that Major Component, and **(b)** serves only to -enable use of the work with that Major Component, or to implement a Standard -Interface for which an implementation is available to the public in source code form. -A “Major Component”, in this context, means a major essential component -(kernel, window system, and so on) of the specific operating system (if any) on which -the executable work runs, or a compiler used to produce the work, or an object code -interpreter used to run it. - -The “Corresponding Source” for a work in object code form means all the -source code needed to generate, install, and (for an executable work) run the object -code and to modify the work, including scripts to control those activities. However, -it does not include the work's System Libraries, or general-purpose tools or -generally available free programs which are used unmodified in performing those -activities but which are not part of the work. For example, Corresponding Source -includes interface definition files associated with source files for the work, and -the source code for shared libraries and dynamically linked subprograms that the work -is specifically designed to require, such as by intimate data communication or -control flow between those subprograms and other parts of the work. - -The Corresponding Source need not include anything that users can regenerate -automatically from other parts of the Corresponding Source. - -The Corresponding Source for a work in source code form is that same work. - -### 2. Basic Permissions - -All rights granted under this License are granted for the term of copyright on the -Program, and are irrevocable provided the stated conditions are met. This License -explicitly affirms your unlimited permission to run the unmodified Program. The -output from running a covered work is covered by this License only if the output, -given its content, constitutes a covered work. This License acknowledges your rights -of fair use or other equivalent, as provided by copyright law. - -You may make, run and propagate covered works that you do not convey, without -conditions so long as your license otherwise remains in force. You may convey covered -works to others for the sole purpose of having them make modifications exclusively -for you, or provide you with facilities for running those works, provided that you -comply with the terms of this License in conveying all material for which you do not -control copyright. Those thus making or running the covered works for you must do so -exclusively on your behalf, under your direction and control, on terms that prohibit -them from making any copies of your copyrighted material outside their relationship -with you. - -Conveying under any other circumstances is permitted solely under the conditions -stated below. Sublicensing is not allowed; section 10 makes it unnecessary. - -### 3. Protecting Users' Legal Rights From Anti-Circumvention Law - -No covered work shall be deemed part of an effective technological measure under any -applicable law fulfilling obligations under article 11 of the WIPO copyright treaty -adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention -of such measures. - -When you convey a covered work, you waive any legal power to forbid circumvention of -technological measures to the extent such circumvention is effected by exercising -rights under this License with respect to the covered work, and you disclaim any -intention to limit operation or modification of the work as a means of enforcing, -against the work's users, your or third parties' legal rights to forbid circumvention -of technological measures. - -### 4. Conveying Verbatim Copies - -You may convey verbatim copies of the Program's source code as you receive it, in any -medium, provided that you conspicuously and appropriately publish on each copy an -appropriate copyright notice; keep intact all notices stating that this License and -any non-permissive terms added in accord with section 7 apply to the code; keep -intact all notices of the absence of any warranty; and give all recipients a copy of -this License along with the Program. - -You may charge any price or no price for each copy that you convey, and you may offer -support or warranty protection for a fee. - -### 5. Conveying Modified Source Versions - -You may convey a work based on the Program, or the modifications to produce it from -the Program, in the form of source code under the terms of section 4, provided that -you also meet all of these conditions: - -* **a)** The work must carry prominent notices stating that you modified it, and giving a -relevant date. -* **b)** The work must carry prominent notices stating that it is released under this -License and any conditions added under section 7. This requirement modifies the -requirement in section 4 to “keep intact all notices”. -* **c)** You must license the entire work, as a whole, under this License to anyone who -comes into possession of a copy. This License will therefore apply, along with any -applicable section 7 additional terms, to the whole of the work, and all its parts, -regardless of how they are packaged. This License gives no permission to license the -work in any other way, but it does not invalidate such permission if you have -separately received it. -* **d)** If the work has interactive user interfaces, each must display Appropriate Legal -Notices; however, if the Program has interactive interfaces that do not display -Appropriate Legal Notices, your work need not make them do so. - -A compilation of a covered work with other separate and independent works, which are -not by their nature extensions of the covered work, and which are not combined with -it such as to form a larger program, in or on a volume of a storage or distribution -medium, is called an “aggregate” if the compilation and its resulting -copyright are not used to limit the access or legal rights of the compilation's users -beyond what the individual works permit. Inclusion of a covered work in an aggregate -does not cause this License to apply to the other parts of the aggregate. - -### 6. Conveying Non-Source Forms - -You may convey a covered work in object code form under the terms of sections 4 and -5, provided that you also convey the machine-readable Corresponding Source under the -terms of this License, in one of these ways: - -* **a)** Convey the object code in, or embodied in, a physical product (including a -physical distribution medium), accompanied by the Corresponding Source fixed on a -durable physical medium customarily used for software interchange. -* **b)** Convey the object code in, or embodied in, a physical product (including a -physical distribution medium), accompanied by a written offer, valid for at least -three years and valid for as long as you offer spare parts or customer support for -that product model, to give anyone who possesses the object code either **(1)** a copy of -the Corresponding Source for all the software in the product that is covered by this -License, on a durable physical medium customarily used for software interchange, for -a price no more than your reasonable cost of physically performing this conveying of -source, or **(2)** access to copy the Corresponding Source from a network server at no -charge. -* **c)** Convey individual copies of the object code with a copy of the written offer to -provide the Corresponding Source. This alternative is allowed only occasionally and -noncommercially, and only if you received the object code with such an offer, in -accord with subsection 6b. -* **d)** Convey the object code by offering access from a designated place (gratis or for -a charge), and offer equivalent access to the Corresponding Source in the same way -through the same place at no further charge. You need not require recipients to copy -the Corresponding Source along with the object code. If the place to copy the object -code is a network server, the Corresponding Source may be on a different server -(operated by you or a third party) that supports equivalent copying facilities, -provided you maintain clear directions next to the object code saying where to find -the Corresponding Source. Regardless of what server hosts the Corresponding Source, -you remain obligated to ensure that it is available for as long as needed to satisfy -these requirements. -* **e)** Convey the object code using peer-to-peer transmission, provided you inform -other peers where the object code and Corresponding Source of the work are being -offered to the general public at no charge under subsection 6d. - -A separable portion of the object code, whose source code is excluded from the -Corresponding Source as a System Library, need not be included in conveying the -object code work. - -A “User Product” is either **(1)** a “consumer product”, which -means any tangible personal property which is normally used for personal, family, or -household purposes, or **(2)** anything designed or sold for incorporation into a -dwelling. In determining whether a product is a consumer product, doubtful cases -shall be resolved in favor of coverage. For a particular product received by a -particular user, “normally used” refers to a typical or common use of -that class of product, regardless of the status of the particular user or of the way -in which the particular user actually uses, or expects or is expected to use, the -product. A product is a consumer product regardless of whether the product has -substantial commercial, industrial or non-consumer uses, unless such uses represent -the only significant mode of use of the product. - -“Installation Information” for a User Product means any methods, -procedures, authorization keys, or other information required to install and execute -modified versions of a covered work in that User Product from a modified version of -its Corresponding Source. The information must suffice to ensure that the continued -functioning of the modified object code is in no case prevented or interfered with -solely because modification has been made. - -If you convey an object code work under this section in, or with, or specifically for -use in, a User Product, and the conveying occurs as part of a transaction in which -the right of possession and use of the User Product is transferred to the recipient -in perpetuity or for a fixed term (regardless of how the transaction is -characterized), the Corresponding Source conveyed under this section must be -accompanied by the Installation Information. But this requirement does not apply if -neither you nor any third party retains the ability to install modified object code -on the User Product (for example, the work has been installed in ROM). - -The requirement to provide Installation Information does not include a requirement to -continue to provide support service, warranty, or updates for a work that has been -modified or installed by the recipient, or for the User Product in which it has been -modified or installed. Access to a network may be denied when the modification itself -materially and adversely affects the operation of the network or violates the rules -and protocols for communication across the network. - -Corresponding Source conveyed, and Installation Information provided, in accord with -this section must be in a format that is publicly documented (and with an -implementation available to the public in source code form), and must require no -special password or key for unpacking, reading or copying. - -### 7. Additional Terms - -“Additional permissions” are terms that supplement the terms of this -License by making exceptions from one or more of its conditions. Additional -permissions that are applicable to the entire Program shall be treated as though they -were included in this License, to the extent that they are valid under applicable -law. If additional permissions apply only to part of the Program, that part may be -used separately under those permissions, but the entire Program remains governed by -this License without regard to the additional permissions. - -When you convey a copy of a covered work, you may at your option remove any -additional permissions from that copy, or from any part of it. (Additional -permissions may be written to require their own removal in certain cases when you -modify the work.) You may place additional permissions on material, added by you to a -covered work, for which you have or can give appropriate copyright permission. - -Notwithstanding any other provision of this License, for material you add to a -covered work, you may (if authorized by the copyright holders of that material) -supplement the terms of this License with terms: - -* **a)** Disclaiming warranty or limiting liability differently from the terms of -sections 15 and 16 of this License; or -* **b)** Requiring preservation of specified reasonable legal notices or author -attributions in that material or in the Appropriate Legal Notices displayed by works -containing it; or -* **c)** Prohibiting misrepresentation of the origin of that material, or requiring that -modified versions of such material be marked in reasonable ways as different from the -original version; or -* **d)** Limiting the use for publicity purposes of names of licensors or authors of the -material; or -* **e)** Declining to grant rights under trademark law for use of some trade names, -trademarks, or service marks; or -* **f)** Requiring indemnification of licensors and authors of that material by anyone -who conveys the material (or modified versions of it) with contractual assumptions of -liability to the recipient, for any liability that these contractual assumptions -directly impose on those licensors and authors. - -All other non-permissive additional terms are considered “further -restrictions” within the meaning of section 10. If the Program as you received -it, or any part of it, contains a notice stating that it is governed by this License -along with a term that is a further restriction, you may remove that term. If a -license document contains a further restriction but permits relicensing or conveying -under this License, you may add to a covered work material governed by the terms of -that license document, provided that the further restriction does not survive such -relicensing or conveying. - -If you add terms to a covered work in accord with this section, you must place, in -the relevant source files, a statement of the additional terms that apply to those -files, or a notice indicating where to find the applicable terms. - -Additional terms, permissive or non-permissive, may be stated in the form of a -separately written license, or stated as exceptions; the above requirements apply -either way. - -### 8. Termination - -You may not propagate or modify a covered work except as expressly provided under -this License. Any attempt otherwise to propagate or modify it is void, and will -automatically terminate your rights under this License (including any patent licenses -granted under the third paragraph of section 11). - -However, if you cease all violation of this License, then your license from a -particular copyright holder is reinstated **(a)** provisionally, unless and until the -copyright holder explicitly and finally terminates your license, and **(b)** permanently, -if the copyright holder fails to notify you of the violation by some reasonable means -prior to 60 days after the cessation. - -Moreover, your license from a particular copyright holder is reinstated permanently -if the copyright holder notifies you of the violation by some reasonable means, this -is the first time you have received notice of violation of this License (for any -work) from that copyright holder, and you cure the violation prior to 30 days after -your receipt of the notice. - -Termination of your rights under this section does not terminate the licenses of -parties who have received copies or rights from you under this License. If your -rights have been terminated and not permanently reinstated, you do not qualify to -receive new licenses for the same material under section 10. - -### 9. Acceptance Not Required for Having Copies - -You are not required to accept this License in order to receive or run a copy of the -Program. Ancillary propagation of a covered work occurring solely as a consequence of -using peer-to-peer transmission to receive a copy likewise does not require -acceptance. However, nothing other than this License grants you permission to -propagate or modify any covered work. These actions infringe copyright if you do not -accept this License. Therefore, by modifying or propagating a covered work, you -indicate your acceptance of this License to do so. - -### 10. Automatic Licensing of Downstream Recipients - -Each time you convey a covered work, the recipient automatically receives a license -from the original licensors, to run, modify and propagate that work, subject to this -License. You are not responsible for enforcing compliance by third parties with this -License. - -An “entity transaction” is a transaction transferring control of an -organization, or substantially all assets of one, or subdividing an organization, or -merging organizations. If propagation of a covered work results from an entity -transaction, each party to that transaction who receives a copy of the work also -receives whatever licenses to the work the party's predecessor in interest had or -could give under the previous paragraph, plus a right to possession of the -Corresponding Source of the work from the predecessor in interest, if the predecessor -has it or can get it with reasonable efforts. - -You may not impose any further restrictions on the exercise of the rights granted or -affirmed under this License. For example, you may not impose a license fee, royalty, -or other charge for exercise of rights granted under this License, and you may not -initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging -that any patent claim is infringed by making, using, selling, offering for sale, or -importing the Program or any portion of it. - -### 11. Patents - -A “contributor” is a copyright holder who authorizes use under this -License of the Program or a work on which the Program is based. The work thus -licensed is called the contributor's “contributor version”. - -A contributor's “essential patent claims” are all patent claims owned or -controlled by the contributor, whether already acquired or hereafter acquired, that -would be infringed by some manner, permitted by this License, of making, using, or -selling its contributor version, but do not include claims that would be infringed -only as a consequence of further modification of the contributor version. For -purposes of this definition, “control” includes the right to grant patent -sublicenses in a manner consistent with the requirements of this License. - -Each contributor grants you a non-exclusive, worldwide, royalty-free patent license -under the contributor's essential patent claims, to make, use, sell, offer for sale, -import and otherwise run, modify and propagate the contents of its contributor -version. - -In the following three paragraphs, a “patent license” is any express -agreement or commitment, however denominated, not to enforce a patent (such as an -express permission to practice a patent or covenant not to sue for patent -infringement). To “grant” such a patent license to a party means to make -such an agreement or commitment not to enforce a patent against the party. - -If you convey a covered work, knowingly relying on a patent license, and the -Corresponding Source of the work is not available for anyone to copy, free of charge -and under the terms of this License, through a publicly available network server or -other readily accessible means, then you must either **(1)** cause the Corresponding -Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the -patent license for this particular work, or **(3)** arrange, in a manner consistent with -the requirements of this License, to extend the patent license to downstream -recipients. “Knowingly relying” means you have actual knowledge that, but -for the patent license, your conveying the covered work in a country, or your -recipient's use of the covered work in a country, would infringe one or more -identifiable patents in that country that you have reason to believe are valid. - -If, pursuant to or in connection with a single transaction or arrangement, you -convey, or propagate by procuring conveyance of, a covered work, and grant a patent -license to some of the parties receiving the covered work authorizing them to use, -propagate, modify or convey a specific copy of the covered work, then the patent -license you grant is automatically extended to all recipients of the covered work and -works based on it. - -A patent license is “discriminatory” if it does not include within the -scope of its coverage, prohibits the exercise of, or is conditioned on the -non-exercise of one or more of the rights that are specifically granted under this -License. You may not convey a covered work if you are a party to an arrangement with -a third party that is in the business of distributing software, under which you make -payment to the third party based on the extent of your activity of conveying the -work, and under which the third party grants, to any of the parties who would receive -the covered work from you, a discriminatory patent license **(a)** in connection with -copies of the covered work conveyed by you (or copies made from those copies), or **(b)** -primarily for and in connection with specific products or compilations that contain -the covered work, unless you entered into that arrangement, or that patent license -was granted, prior to 28 March 2007. - -Nothing in this License shall be construed as excluding or limiting any implied -license or other defenses to infringement that may otherwise be available to you -under applicable patent law. - -### 12. No Surrender of Others' Freedom - -If conditions are imposed on you (whether by court order, agreement or otherwise) -that contradict the conditions of this License, they do not excuse you from the -conditions of this License. If you cannot convey a covered work so as to satisfy -simultaneously your obligations under this License and any other pertinent -obligations, then as a consequence you may not convey it at all. For example, if you -agree to terms that obligate you to collect a royalty for further conveying from -those to whom you convey the Program, the only way you could satisfy both those terms -and this License would be to refrain entirely from conveying the Program. - -### 13. Use with the GNU Affero General Public License - -Notwithstanding any other provision of this License, you have permission to link or -combine any covered work with a work licensed under version 3 of the GNU Affero -General Public License into a single combined work, and to convey the resulting work. -The terms of this License will continue to apply to the part which is the covered -work, but the special requirements of the GNU Affero General Public License, section -13, concerning interaction through a network will apply to the combination as such. - -### 14. Revised Versions of this License - -The Free Software Foundation may publish revised and/or new versions of the GNU -General Public License from time to time. Such new versions will be similar in spirit -to the present version, but may differ in detail to address new problems or concerns. - -Each version is given a distinguishing version number. If the Program specifies that -a certain numbered version of the GNU General Public License “or any later -version” applies to it, you have the option of following the terms and -conditions either of that numbered version or of any later version published by the -Free Software Foundation. If the Program does not specify a version number of the GNU -General Public License, you may choose any version ever published by the Free -Software Foundation. - -If the Program specifies that a proxy can decide which future versions of the GNU -General Public License can be used, that proxy's public statement of acceptance of a -version permanently authorizes you to choose that version for the Program. - -Later license versions may give you additional or different permissions. However, no -additional obligations are imposed on any author or copyright holder as a result of -your choosing to follow a later version. - -### 15. Disclaimer of Warranty - -THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. -EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES -PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER -EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE -QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE -DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - -### 16. Limitation of Liability - -IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY -COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS -PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, -INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE -PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE -OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE -WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE -POSSIBILITY OF SUCH DAMAGES. - -### 17. Interpretation of Sections 15 and 16 - -If the disclaimer of warranty and limitation of liability provided above cannot be -given local legal effect according to their terms, reviewing courts shall apply local -law that most closely approximates an absolute waiver of all civil liability in -connection with the Program, unless a warranty or assumption of liability accompanies -a copy of the Program in return for a fee. - -_END OF TERMS AND CONDITIONS_ - -## How to Apply These Terms to Your New Programs - -If you develop a new program, and you want it to be of the greatest possible use to -the public, the best way to achieve this is to make it free software which everyone -can redistribute and change under these terms. - -To do so, attach the following notices to the program. It is safest to attach them -to the start of each source file to most effectively state the exclusion of warranty; -and each file should have at least the “copyright” line and a pointer to -where the full notice is found. - - - Copyright (C) - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - -Also add information on how to contact you by electronic and paper mail. - -If the program does terminal interaction, make it output a short notice like this -when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type 'show c' for details. - -The hypothetical commands `show w` and `show c` should show the appropriate parts of -the General Public License. Of course, your program's commands might be different; -for a GUI interface, you would use an “about box”. - -You should also get your employer (if you work as a programmer) or school, if any, to -sign a “copyright disclaimer” for the program, if necessary. For more -information on this, and how to apply and follow the GNU GPL, see -<>. - -The GNU General Public License does not permit incorporating your program into -proprietary programs. If your program is a subroutine library, you may consider it -more useful to permit linking proprietary applications with the library. If this is -what you want to do, use the GNU Lesser General Public License instead of this -License. But first, please read -<>. diff --git a/R/adapter_matrix.R b/R/adapter_matrix.R index 43b47e9..ad491ec 100644 --- a/R/adapter_matrix.R +++ b/R/adapter_matrix.R @@ -57,16 +57,15 @@ adapter_matrix <- function( } } value <- match.arg(value, c("pident", "mean_score", "end")) - cl <- parallel::makeCluster(cores, type = "PSOCK") - doParallel::registerDoParallel(cl) - on.exit(parallel::stopCluster(cl), add = TRUE) + dmat <- matrix(NA, nrow = length(ids), ncol = length(ids)) rownames(dmat) = ids colnames(dmat) = ids - dmat <- foreach::foreach( - i = seq_len(nrow(dmat)), .combine = 'rbind',.inorder=TRUE) %dopar% { - i <- i - for (j in seq_len(ncol(dmat))){ + + if (cores == 1) { + # Use regular for loop when cores = 1 + for (i in seq_len(nrow(dmat))) { + for (j in seq_len(ncol(dmat))) { if (i == j) next() adapter <- adapters |> filter_comparisons(ids[i]) |> @@ -79,8 +78,33 @@ adapter_matrix <- function( stop("Multiple comparisons found for ids: ", ids[i], ", ", ids[j], ".") } } - return(dmat[i,]) } + } else { + # Use parallelization when cores > 1 + cl <- parallel::makeCluster(cores, type = "PSOCK") + doParallel::registerDoParallel(cl) + on.exit(parallel::stopCluster(cl), add = TRUE) + + dmat <- foreach::foreach( + i = seq_len(nrow(dmat)), .combine = 'rbind', .inorder = TRUE) %dopar% { + i <- i + for (j in seq_len(ncol(dmat))) { + if (i == j) next() + adapter <- adapters |> + filter_comparisons(ids[i]) |> + filter_comparisons(ids[j]) + if (nrow(adapter) == 0) { + stop("No comparisons found for ids: ", ids[i], ", ", ids[j], ".") + } else if (nrow(adapter) == 1) { + dmat[i, j] <- ifelse(is.na(adapter[[value]]), 0, adapter[[value]]) + } else { + stop("Multiple comparisons found for ids: ", ids[i], ", ", ids[j], ".") + } + } + return(dmat[i, ]) + } + } + if (value == "pident") diag(dmat) <- 1 rownames(dmat) <- ids colnames(dmat) <- ids diff --git a/R/cluster_adapters.R b/R/cluster_adapters.R index d044d0f..3a4c687 100644 --- a/R/cluster_adapters.R +++ b/R/cluster_adapters.R @@ -40,12 +40,22 @@ cluster_adapters <- function( if (is.null(k_max)) k_max <- nrow(mat) - cl <- parallel::makeCluster(cores, type = "PSOCK") - doParallel::registerDoParallel(cl) - on.exit(parallel::stopCluster(cl), add = TRUE) + if (cores == 1) { + # Use regular for loop when cores = 1 + schocos_list <- list() + for (k in k_min:k_max) { + schocos_list[[length(schocos_list) + 1]] <- schoco(mat, k, homogeneity_thr, completeness_thr) + } + schocos <- do.call(rbind, schocos_list) + } else { + # Use parallelization when cores > 1 + cl <- parallel::makeCluster(cores, type = "PSOCK") + doParallel::registerDoParallel(cl) + on.exit(parallel::stopCluster(cl), add = TRUE) - schocos <- foreach::foreach(k = k_min:k_max, .combine = 'rbind') %dopar% { - schoco(mat, k, homogeneity_thr, completeness_thr) + schocos <- foreach::foreach(k = k_min:k_max, .combine = 'rbind') %dopar% { + schoco(mat, k, homogeneity_thr, completeness_thr) + } } schocos <- split(schocos, schocos$nclust) |> unname() diff --git a/R/find_all_adapters.R b/R/find_all_adapters.R index 1815b15..00118e3 100644 --- a/R/find_all_adapters.R +++ b/R/find_all_adapters.R @@ -50,14 +50,10 @@ find_all_adapters <- function( names(pairs) <- c("pattern", "subject") adapters <- data.frame() - cl <- parallel::makeCluster(cores, type = "PSOCK") - doParallel::registerDoParallel(cl) - on.exit(parallel::stopCluster(cl), add = TRUE) - - adapters <- foreach::foreach( - i = seq_len(nrow(pairs)), .combine = 'rbind' - ) %dopar% { - i <- i + if (cores == 1) { + # Use regular for loop when cores = 1 + adapters_list <- list() + for (i in seq_len(nrow(pairs))) { pattern <- pairs$pattern[i] subject <- pairs$subject[i] ps <- position_scores( @@ -76,8 +72,41 @@ find_all_adapters <- function( start_threshold = start_threshold, merge = merge ) - return(adapter) + adapters_list[[i]] <- adapter + } + adapters <- do.call(rbind, adapters_list) + } else { + # Use parallelization when cores > 1 + cl <- parallel::makeCluster(cores, type = "PSOCK") + doParallel::registerDoParallel(cl) + on.exit(parallel::stopCluster(cl), add = TRUE) + + adapters <- foreach::foreach( + i = seq_len(nrow(pairs)), .combine = 'rbind' + ) %dopar% { + i <- i + pattern <- pairs$pattern[i] + subject <- pairs$subject[i] + ps <- position_scores( + pattern_id = pattern, + subject_id = subject, + id_var = id_var, + seq_var = seq_var, + submat = submat, + data = data, + verbose = verbose + ) + adapter <- ps |> + find_breakpoints(method = method, ...) |> + find_adapter( + pident_threshold = pident_threshold, + start_threshold = start_threshold, + merge = merge + ) + return(adapter) + } } + class(adapters) <- c("adapter", class(adapters)) return(adapters) } diff --git a/README.Rmd b/README.Rmd index 4bdd760..32e55ca 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,13 +22,21 @@ knitr::opts_chunk$set( [![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R build status](https://github.com/sbthandras/tailor/workflows/R-CMD-check/badge.svg)](https://github.com/sbthandras/tailor/actions) -[![Coverage](https://codecov.io/github/sbthandras/tailor/coverage.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) +[![Coverage](https://codecov.io/github/sbthandras/tailor/graph/badge.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) [![DOI](https://img.shields.io/badge/DOI-10.64898%2F2026.02.20.706991-blue)](https://doi.org/10.64898/2026.02.20.706991) `tailor` is a **T**ool for **A**dapter-domain **I**dentification and **L**inking **O**f **R**BPs. +# IMPORANT NOTICE + +The latest version of this repository was publised in https://github.com/sbthandras/tailor on 2 March 2026. + +Following publication this development repository was archived. + +Please refer to https://github.com/sbthandras/tailor for the latest version of the package and documentation. + ## Installation #### Install from Github (development version) diff --git a/README.md b/README.md index 54f1ad8..e838ed1 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ [![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R build status](https://github.com/sbthandras/tailor/workflows/R-CMD-check/badge.svg)](https://github.com/sbthandras/tailor/actions) -[![Coverage](https://codecov.io/github/sbthandras/tailor/coverage.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) +[![Coverage](https://codecov.io/github/sbthandras/tailor/graph/badge.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) [![DOI](https://img.shields.io/badge/DOI-10.64898%2F2026.02.20.706991-blue)](https://doi.org/10.64898/2026.02.20.706991) @@ -16,6 +16,16 @@ status](https://github.com/sbthandras/tailor/workflows/R-CMD-check/badge.svg)](h `tailor` is a **T**ool for **A**dapter-domain **I**dentification and **L**inking **O**f **R**BPs. +# IMPORANT NOTICE + +The latest version of this repository was publised in + on 2 March 2026. + +Following publication this development repository was archived. + +Please refer to for the latest +version of the package and documentation. + ## Installation #### Install from Github (development version) diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..28f24b9 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(tailor) + +test_check("tailor")