diff --git a/.Rbuildignore b/.Rbuildignore
index 4b3f9f2c270555351c5f4e1add8695d20d52e894..b69480f327595e22c7f4b5bf11591725ce79295f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,8 @@
^.*\.Rproj$
^\.Rproj\.user$
^data-raw$
+^man-roxygen$
+^LICENSE\.md$
+[.]INI$
+^\.gitlab-ci\.yml$
+^ci$
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d333e279f7bfeb700598f835e6267da7b1958b4d
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,32 @@
+stages:
+ - check
+
+variables:
+ R_CI: "$CI_PROJECT_DIR/ci"
+ R_LIBS_USER: "$R_CI/lib"
+
+default:
+ tags: [docker]
+ image: rocker/verse:devel
+
+cache:
+ paths:
+ - $R_CI
+
+before_script:
+ - mkdir -p $R_LIBS_USER
+ - echo "R_LIBS='$R_LIBS_USER'" > .Renviron
+ - sudo apt-get update && sudo apt-get install -y libudunits2-dev proj-bin libgdal-dev libgeos-dev
+ - R -q -e 'remotes::install_deps(dependencies = TRUE)'
+
+check:
+ stage: check
+ script:
+ - tlmgr update --self && tlmgr install ec epstopdf-pkg
+ - R -q -e 'remotes::update_packages("rcmdcheck")'
+ - R -q -e 'rcmdcheck::rcmdcheck(args = "--as-cran", error_on = "error")'
+
+test_all:
+ stage: check
+ script:
+ - R -q -e 'devtools::test()'
diff --git a/DESCRIPTION b/DESCRIPTION
index 774286d5002a07115751a262eebe3efc9d899dff..b37335b156e5a21d8e8f919f62281467ee9b2111 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -6,18 +6,23 @@ Authors@R: c(
person("David", "Dorchies", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6595-7984"), email = "david.dorchies@inrae.fr")
)
Description: SIC^2 software (Simulation and Integration of Control for Canals (or Channels)) is a hydraulic simulation software adapted to the calculation of flows in irrigation canals, rivers and sewage systems (<https://sic.g-eau.fr/>). This package provides functions to automate the use of SIC2 with R.
-License: What license is it under?
+License: AGPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests:
R.utils,
RandomFields,
- testthat (>= 3.0.0)
+ testthat (>= 3.0.0),
+ yaml
Config/testthat/edition: 3
Depends:
R (>= 2.10)
RoxygenNote: 7.1.2
Roxygen: list(markdown = TRUE)
Imports:
+ config,
logger,
- terra
+ magrittr,
+ terra,
+ tidyquery,
+ xml2
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000000000000000000000000000000000000..fab6548ec038593073aaa735e58003e9575728e9
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,659 @@
+GNU Affero General Public License
+=================================
+
+_Version 3, 19 November 2007_
+_Copyright (C) 2007 Free Software Foundation, Inc. <<https://fsf.org/>>_
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+## Preamble
+
+The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
+
+The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+our General Public Licenses are 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.
+
+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.
+
+Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
+
+A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate. Many developers of free software are heartened and
+encouraged by the resulting cooperation. However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
+
+The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community. It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server. Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing
+under this license.
+
+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 Affero 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
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+interfaces specified for a particular programming language, one that
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+
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+than the work as a whole, that (a) is included in the normal form of
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+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
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+produce the work, or an object code interpreter used to run it.
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+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
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+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
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+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
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+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
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+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).
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+installed. Access to a network may be denied when the modification
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+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.
+
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+add to a covered work, you may (if authorized by the copyright holders
+of that material) supplement the terms of this License with terms:
+
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+ terms of sections 15 and 16 of this License; or
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+ 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
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+ material by anyone who conveys the material (or modified versions
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+
+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
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+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.
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+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
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+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. Remote Network Interaction; Use with the GNU General Public License.
+
+Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your
+version supports such interaction) an opportunity to receive the
+Corresponding Source of your version by providing access to the
+Corresponding Source from a network server at no charge, through some
+standard or customary means of facilitating copying of software. This
+Corresponding Source shall include the Corresponding Source for any
+work covered by version 3 of the GNU General Public License that is
+incorporated pursuant to the following paragraph.
+
+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 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 work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+### 14. Revised Versions of this License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Affero 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 Affero 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 Affero 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 Affero 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.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero 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 Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper
+mail.
+
+If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for
+the specific requirements.
+
+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 AGPL, see <https://www.gnu.org/licenses/>.
diff --git a/NAMESPACE b/NAMESPACE
index 72481a1d7375a173b8f25c13d23630404684a49f..af76d821d72f8da42d0930dd0ea697cb48241e95 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
# Generated by roxygen2: do not edit by hand
+export(cfg_tmp_project)
export(convert_sic_params)
export(create_section_txt)
export(create_uniform_reach_txt)
@@ -7,10 +8,18 @@ export(dem_to_reach)
export(dem_to_reach_txt)
export(dem_to_section)
export(extract_reach)
+export(get_result)
+export(get_result_tree)
export(get_section_centers)
export(loadConfig)
export(merge_reaches)
+export(read_bin_result_matrix)
export(set_initial_conditions)
+export(sic_import_reaches)
export(sic_run_export)
export(sic_run_fortran)
export(split_reach)
+import(magrittr)
+import(utils)
+import(xml2)
+importFrom(stats,dist)
diff --git a/R/cfg_tmp_project.R b/R/cfg_tmp_project.R
new file mode 100644
index 0000000000000000000000000000000000000000..4ff341b6eaccd9f7693ae3394eae78cf3ec718f7
--- /dev/null
+++ b/R/cfg_tmp_project.R
@@ -0,0 +1,21 @@
+#' Set a configuration with a temporary project directory
+#'
+#' @param xml_path [character], the path of the XML SIC project file
+#' @param cfg [config], the configuration to modify
+#'
+#' @return The updated configuration with the temporary project directory
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' cfg <- cfg_tmp_project()
+#' cfg$project$xml_path
+#' }
+#'
+cfg_tmp_project <- function(xml_path = system.file("sic_project_test1.xml", package = "rsic2"), cfg = loadConfig(xml_path = xml_path)) {
+ cfg$project$path <- tempfile("sic_project", fileext = ".xml")
+ file.copy(xml_path,
+ cfg$project$path,
+ overwrite = TRUE)
+ return(cfg)
+}
diff --git a/R/convert_sic_params.R b/R/convert_sic_params.R
index 7b674e60199df0b2b90505c7433292366df9feed..2d8a24a3502845109d6b1affcfd34e652085b91e 100644
--- a/R/convert_sic_params.R
+++ b/R/convert_sic_params.R
@@ -11,8 +11,10 @@
#' @export
#'
#' @examples
-#' convert_sic_params(list(SCE = 1, VAR = 1))
-#'
+#' \dontrun{
+#' cfg <- cfg_tmp_project()
+#' convert_sic_params(list(SCE = 1, VAR = 1), cfg = cfg)
+#' }
convert_sic_params <- function(params, cfg = loadConfig()) {
if (!"INTERF" %in% names(params)) {
params <- c(list(INTERF = cfg$sic$fortran$prms$INTERF), params)
diff --git a/R/create_section_txt.R b/R/create_section_txt.R
index 8f38a251869d5d95b1c4e5bff00a623df577e3d3..cd049c6f392d8df2863628771738c6b03a342a30 100644
--- a/R/create_section_txt.R
+++ b/R/create_section_txt.R
@@ -8,9 +8,10 @@
#'
#' @return [character], section description in SIC text import format.
#' @export
+#' @import utils
#' @examples
#' # Trapezoidal section
-#' export_section_txt("Trapeze", 0, "T", list(B = 2, S = 1.5, ZF = 100, ZB = 102))
+#' create_section_txt("Trapeze", 0, "T", list(B = 2, S = 1.5, ZF = 100, ZB = 102))
create_section_txt <- function(section_name, abscissa, section_type, profile, distance_majeur = FALSE) {
if (section_type == "T") {
diff --git a/R/create_uniform_reach_txt.R b/R/create_uniform_reach_txt.R
index 2594e8cfe0b117f4a41886eb5cc350f2ff6ec269..f003d0aab5cb74e9c4cafb0dfb70cb0031180886 100644
--- a/R/create_uniform_reach_txt.R
+++ b/R/create_uniform_reach_txt.R
@@ -3,7 +3,7 @@
#' @param abscissas [numeric] vector of section abscissas
#' @param upstream_bed_elevation [numeric], upstream bed elevation (m)
#' @param slope [numeric], bed slope of the reach (m/m)
-#' @param names [character] vector of section names
+#' @param section_names [character] vector of section names
#' @inheritParams create_section_txt
#'
#' @return A [list] from which each item is a section exported by [create_section_txt].
diff --git a/R/dem_to_reach.R b/R/dem_to_reach.R
index 173139f94bad9145c9664c17b3907d4375ce2ea6..135059303245093201a3f035046510082c1e5d45 100644
--- a/R/dem_to_reach.R
+++ b/R/dem_to_reach.R
@@ -10,9 +10,10 @@
#' @param start 1-length [numeric], starting value for the chainage (i.e. section abscissa) along the reach
#' @param major_bed [logical], `TRUE` for major bed, `FALSE` for minor-medium bed
#'
-#' @return
+#' @return A *ReachTxt* object which is a [list] of *SectionTxt* objects (see [create_section_txt]).
#' @rdname dem_to_reach
#' @export
+#' @importFrom stats dist
#'
#' @examples
#' ## Inputs preparation
@@ -60,7 +61,9 @@ dem_to_reach_txt <- function(dem, node_coords, space_step, section_width, nb_poi
return(reach_txt)
}
+
#' @rdname dem_to_reach
+#' @param section_centers See return value of [get_section_centers]
#' @export
dem_to_reach <- function(dem, node_coords, section_centers, section_width, nb_points = 50) {
lapply(seq_len(nrow(section_centers)), function(i) {
@@ -75,7 +78,7 @@ dem_to_reach <- function(dem, node_coords, section_centers, section_width, nb_po
#' @inheritParams dem_to_reach
#' @param section_center 2-lenght [numeric], coordinates of the section center
#'
-#' @return
+#' @return A [matrix] with the coordinates of the x-z points in the cross-profile section referential
#' @export
#'
#' @inherit dem_to_reach return examples
diff --git a/R/get_result.R b/R/get_result.R
new file mode 100644
index 0000000000000000000000000000000000000000..dea3db655cbabb3790c093abbb26a5013e5e9552
--- /dev/null
+++ b/R/get_result.R
@@ -0,0 +1,169 @@
+#' Get a selection of variables from a simulation result
+#'
+#' @inheritParams sic_run_export
+#' @param filters [character] conditions to select columns in result table, see details
+#' @param m [matrix] of results produced by [read_bin_result_matrix]
+#'
+#' @return [matrix] of results with columns selected by `filters`.
+#' @export
+#' @import magrittr
+#'
+#' @examples
+#' \dontrun{
+#' cfg <- cfg_tmp_project()
+#' sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+#' get_result(cfg, 1, filters = c("bf==4", "var=='Z'"))
+#' }
+get_result <- function(cfg,
+ scenario,
+ variant = 0,
+ filters = c(""),
+ m = read_bin_result_matrix(cfg, scenario, variant)) {
+
+ df_col <- get_result_tree(cfg, scenario, variant)
+ filters <- paste(filters, collapse = " AND ")
+ if (filters != "") {
+ df_col %<>% tidyquery::query(paste("SELECT * WHERE", filters))
+ }
+ m <- m[, df_col$col, drop = FALSE]
+ column_names <- sapply(seq_len(nrow(df_col)),
+ function(i) {
+ df_col$col <- NULL
+ cols <- sapply(names(df_col),
+ function(name) {
+ if (df_col[i, name] > 0) {
+ paste(name, df_col[i, name], sep = ":")
+ } else {
+ NULL
+ }
+ })
+ cols[sapply(cols, is.null)] <- NULL
+ paste(cols, collapse = "|")
+ })
+ colnames(m) <- column_names
+ return(m)
+}
+
+
+#' Read matrix of SIC simulation result file
+#'
+#' @inheritParams sic_run_export
+#'
+#' @return [matrix] with the simulation results
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' cfg <- cfg_tmp_project()
+#' sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+#' m <- read_bin_result_matrix(cfg, 1)
+#' str(m)
+#' }
+read_bin_result_matrix <- function(cfg, scenario, variant = 0) {
+ file <- paste0(
+ paste(gsub("\\.xml", "", cfg$project$path),
+ scenario, variant, sep = "_"),
+ ".res"
+ )
+ con = file(file, "rb")
+ # Skip header
+ readBin(con, "raw", n = 4 * 5 + 4 + 8 + 4 + 4)
+ dims <-
+ readBin(con,
+ "integer",
+ n = 2,
+ size = 4,
+ endian = "little")
+ # Skip (data type code?)
+ readBin(con, "raw", n = 2)
+ data <-
+ readBin(con,
+ "double",
+ n = prod(dims),
+ size = 4,
+ endian = "little")
+ readBin(con, "raw", n = 4) # @todo check end file content
+ close(con)
+ return(matrix(data, ncol = dims[2], byrow = TRUE))
+}
+
+
+#' Get correspondence between network object and columns in result binary file
+#'
+#' @inheritParams sic_run_export
+#'
+#' @return a [data.frame] with following columns:
+#'
+#' - "bf", "sn", "nd", "pr", "ouv": location of the result with number of respectively reach, section, node, offtake, and device.
+#' - "var": the name of the calculated variable
+#' - "col": the column number in the matrix produced by [read_bin_result_matrix]
+#'
+#' @warning
+#' Up to now, this function only handle results at sections.
+#'
+#' @export
+#' @import xml2
+#' @import magrittr
+#'
+#' @examples
+#' \dontrun{
+#' cfg <- cfg_tmp_project()
+#' sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+#' df <- get_result_tree(cfg, 1)
+#' head(df)
+#' }
+get_result_tree <- function(cfg, scenario, variant = 0) {
+ x <- read_xml(cfg$project$path)
+ objs = c("Ouvrage", "Section", "Prise", "Noeud")
+ names(objs) <- objs
+ defcol <- get_DefCol(x, scenario, variant)
+
+ df <- data.frame(bf = integer(),
+ sn = integer(),
+ nd = integer(),
+ pr = integer(),
+ ouv = integer(),
+ var = character(),
+ col = integer())
+
+ # Sections
+ xpath_biefs <- "/Reseau/Liste_Biefs/Bief"
+
+ for (iBf in seq_along(xml_find_all(x, xpath_biefs))) {
+ xpath_sections <- paste0(xpath_biefs, sprintf("[@Num=%d]/Liste_Sections/SectionMin", iBf))
+ for (iSn in seq_along(xml_find_all(x, xpath_sections))) {
+ xpath_res <- paste0(xpath_sections, "[@Num=%d]/Flu[@nScenario=%d]/ListeRes/Res[@nVar=%d]") %>%
+ sprintf(iSn, scenario, variant)
+ cols <- x %>% xml_find_first(xpath_res) %>%
+ xml_attr("nCol") %>% strsplit(":") %>% "[["(1) %>% as.integer
+ cols <- seq(from = cols[1], length.out = cols[2])
+
+ df %<>% result_tree_add(list(bf = iBf, sn = iSn),
+ defcol$Section,
+ cols)
+ }
+ }
+ return(df)
+}
+
+result_tree_add <- function(df, loc, defcol, cols) {
+ loc <- modifyList(list(bf = 0, sn = 0, nd = 0, pr = 0, ouv = 0),
+ loc)
+ return(rbind(df, data.frame(as.data.frame(loc), var = defcol, col = cols)))
+}
+
+get_DefCol <-
+ function(x,
+ scenario,
+ variant,
+ xpath = "/Reseau/Flu[@nScenario=%d]/ListeRes/Res[@nVar=%d]/ListeDefCol/DefCol[@Objet=\"%s\"]",
+ objs = c("Ouvrage", "Section", "Prise", "Noeud")) {
+ names(objs) <- objs
+ lapply(objs, function(obj)
+ get_text_xml_path(x, xpath, scenario, variant, obj))
+ }
+
+get_text_xml_path <- function(x, xpath, scenario, var, obj) {
+ x %>% xml_find_first(xpath = sprintf(xpath, scenario, var, obj)) %>%
+ xml_text %>% strsplit("\t") %>% "[["(1)
+}
diff --git a/R/merge_reaches.R b/R/merge_reaches.R
index dd3b31753f1de4b639ad7e1b8493ffa22c9ea667..16c31059b00be40e21ea0f6273e8afe072ca6148 100644
--- a/R/merge_reaches.R
+++ b/R/merge_reaches.R
@@ -1,8 +1,8 @@
-#' Merge several ReachTxt objects into one
+#' Merge several *ReachTxt* objects into one
#'
-#' @param ... ReachTxt objects
+#' @param ... *ReachTxt* objects
#'
-#' @return
+#' @return a *ReachTxt* object (See [create_uniform_reach_txt] and [dem_to_reach]) containing the merged reaches.
#' @export
#'
#' @examples
diff --git a/R/sic_import_reaches.R b/R/sic_import_reaches.R
index d363252820e53d2b2f70e24e7f20f7145467d20f..71c1a2e073875d77132f979fec035dbe5aee5450 100644
--- a/R/sic_import_reaches.R
+++ b/R/sic_import_reaches.R
@@ -1,3 +1,38 @@
+#' Import reach geometries into a SIC project
+#'
+#' @param reaches A [list] of ReachTxt objects (See [split_reach])
+#' @param import_mode [character], importation mode of EdiSIC (See \url{https://sic.g-eau.fr/Import-sections-in-text-format?lang=en#import-modes-2})
+#' @template param_cfg
+#'
+#' @return A [numeric] code returned by [shell]
+#' @export
+#'
+#' @examples
+#' # Minor bed generation
+#' profT <- matrix(c(2, 6, 0, 2), ncol = 2)
+#' min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+#' upstream_bed_elevation = 8 + 10000 * 0.002,
+#' slope = 0.002,
+#' section_type = "L",
+#' profile = profT)
+#'
+#' # Major bed generation
+#' data("floodam_ead_dem")
+#' dem <- terra::rast(floodam_ead_dem)
+#' node_coords <- matrix(c(102550, 102550, 110000, 100000), ncol = 2)
+#' space_step = 100
+#' section_width = 5000
+#' maj_reach <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+#'
+#' # Merge minor and major beds and split into 2 reaches
+#' reach <- merge_reaches(min_reach, maj_reach)
+#' reaches <- split_reach(reach, seq(0, 10000, 5000))
+#'
+#' \dontrun{
+#' # Import with EdiSic
+#' cfg <- cfg_tmp_project()
+#' sic_import_reaches(reaches, cfg = cfg)
+#' }
sic_import_reaches <- function(reaches, import_mode = "ImportXml_UPDATE", cfg = loadConfig()) {
# Create reach files
import_path <- dirname(cfg$project$path)
diff --git a/R/sic_run_fortran.R b/R/sic_run_fortran.R
index 57c986a5f2638ea89b9c54d017cc262ccdd89698..cb649c5f976be647b5ddc7c02c74e227a23eb267 100644
--- a/R/sic_run_fortran.R
+++ b/R/sic_run_fortran.R
@@ -7,14 +7,15 @@
#' @details If argument `params` is a [list], arguments are injected in the command line by taking the items of the list with the conversion
#' `[key]=[value]`. If argument `params` is a [character]
#'
-#' @return
+#' @return Error code returned by [shell].
#' @export
#'
#' @examples
#' \dontrun{
#' # Run steady simulation for the scenario #1
+#' cfg <- cfg_tmp_project()
#' params <- list(SCE=1)
-#' sic_run_fortran("fluvia", params)
+#' sic_run_fortran("fluvia", params, cfg = cfg)
#'}
sic_run_fortran <- function(prog, params = list(), cfg = loadConfig()) {
if (is.list(params)) params <- convert_sic_params(params, cfg)
@@ -27,9 +28,11 @@ sic_run_fortran <- function(prog, params = list(), cfg = loadConfig()) {
type = "cmd2"
)
logger::log_debug(cmd_line)
- shell(
+ ret <- shell(
cmd_line,
wait = T,
translate = T
)
+ file.remove("FLUVIA.INI", "SIRENE.INI")
+ return(ret)
}
diff --git a/man/cfg_tmp_project.Rd b/man/cfg_tmp_project.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..a1245502dcf5cfec9248b5613f4947c5d971cbf3
--- /dev/null
+++ b/man/cfg_tmp_project.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cfg_tmp_project.R
+\name{cfg_tmp_project}
+\alias{cfg_tmp_project}
+\title{Set a configuration with a temporary project directory}
+\usage{
+cfg_tmp_project(
+ xml_path = system.file("sic_project_test1.xml", package = "rsic2"),
+ cfg = loadConfig(xml_path = xml_path)
+)
+}
+\arguments{
+\item{xml_path}{\link{character}, the path of the XML SIC project file}
+
+\item{cfg}{\link{config}, the configuration to modify}
+}
+\value{
+The updated configuration with the temporary project directory
+}
+\description{
+Set a configuration with a temporary project directory
+}
+\examples{
+\dontrun{
+cfg <- cfg_tmp_project()
+cfg$project$xml_path
+}
+
+}
diff --git a/man/convert_sic_params.Rd b/man/convert_sic_params.Rd
index f41705ec22b831b295d1bf774cd404d1ce0ad067..a861cea558378a3203e2be5f81c945cdc0b06deb 100644
--- a/man/convert_sic_params.Rd
+++ b/man/convert_sic_params.Rd
@@ -21,6 +21,8 @@ This function is called by \link{sic_run_fortran} to convert list of parameters
The parameter \code{INTERF} is set to 0 (zero) by default.
}
\examples{
-convert_sic_param(list(SCE = 1, VAR = 1))
-
+\dontrun{
+cfg <- cfg_tmp_project()
+convert_sic_params(list(SCE = 1, VAR = 1), cfg = cfg)
+}
}
diff --git a/man/create_section_txt.Rd b/man/create_section_txt.Rd
index cd02ce1b2d7cc5467c1f085432653c477936510d..eecc674e690e2eb823d5a955191a8cfe436ede8a 100644
--- a/man/create_section_txt.Rd
+++ b/man/create_section_txt.Rd
@@ -31,5 +31,5 @@ Export a section in importation SIC format
}
\examples{
# Trapezoidal section
-export_section_txt("Trapeze", 0, "T", list(B = 2, S = 1.5, ZF = 100, ZB = 102))
+create_section_txt("Trapeze", 0, "T", list(B = 2, S = 1.5, ZF = 100, ZB = 102))
}
diff --git a/man/create_uniform_reach_txt.Rd b/man/create_uniform_reach_txt.Rd
index f47a6405f510c7dafba40ecfe942730cfaccfcda..64040f86eb3c7a2ba93a99573081a8a5eeab5f1a 100644
--- a/man/create_uniform_reach_txt.Rd
+++ b/man/create_uniform_reach_txt.Rd
@@ -24,7 +24,7 @@ create_uniform_reach_txt(
\item{profile}{\link{list} or \link{matrix}, profile of the section (See details)}
-\item{names}{\link{character} vector of section names}
+\item{section_names}{\link{character} vector of section names}
}
\value{
A \link{list} from which each item is a section exported by \link{create_section_txt}.
diff --git a/man/dem_to_reach.Rd b/man/dem_to_reach.Rd
index 0cbfdd85a49f2bf752e49380292b36390bfd6247..828b099c70a7ecf01245bb6c856e02324ea55c20 100644
--- a/man/dem_to_reach.Rd
+++ b/man/dem_to_reach.Rd
@@ -31,9 +31,11 @@ dem_to_reach(dem, node_coords, section_centers, section_width, nb_points = 50)
\item{start}{1-length \link{numeric}, starting value for the chainage (i.e. section abscissa) along the reach}
\item{major_bed}{\link{logical}, \code{TRUE} for major bed, \code{FALSE} for minor-medium bed}
+
+\item{section_centers}{See return value of \link{get_section_centers}}
}
\value{
-
+A \emph{ReachTxt} object which is a \link{list} of \emph{SectionTxt} objects (see \link{create_section_txt}).
}
\description{
The coordinate system of \code{dem} should be a metric orthonormal coordinate system.
diff --git a/man/dem_to_section.Rd b/man/dem_to_section.Rd
index f3dcd7ec1de8c5b77e0e323a239874e3da02572e..8346460fb318ba141c7abf1f7223d5a3972f2561 100644
--- a/man/dem_to_section.Rd
+++ b/man/dem_to_section.Rd
@@ -18,7 +18,7 @@ dem_to_section(dem, node_coords, section_center, section_width, nb_points = 50)
\item{nb_points}{1-length \link{numeric}, number of points to describe cross-section geometries}
}
\value{
-
+A \link{matrix} with the coordinates of the x-z points in the cross-profile section referential
}
\description{
Create a section cross profile from a DEM
diff --git a/man/get_result.Rd b/man/get_result.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..056115768a5f2a594adaf65f96d921879316c776
--- /dev/null
+++ b/man/get_result.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_result.R
+\name{get_result}
+\alias{get_result}
+\title{Get a selection of variables from a simulation result}
+\usage{
+get_result(
+ cfg,
+ scenario,
+ variant = 0,
+ filters = c(""),
+ m = read_bin_result_matrix(cfg, scenario, variant)
+)
+}
+\arguments{
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+
+\item{scenario}{\link{numeric}, the scenario to read}
+
+\item{variant}{\link{numeric}, the variant to read}
+
+\item{filters}{\link{character} conditions to select columns in result table, see details}
+
+\item{m}{\link{matrix} of results produced by \link{read_bin_result_matrix}}
+}
+\value{
+\link{matrix} of results with columns selected by \code{filters}.
+}
+\description{
+Get a selection of variables from a simulation result
+}
+\examples{
+\dontrun{
+cfg <- cfg_tmp_project()
+sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+get_result(cfg, 1, filters = c("bf==4", "var=='Z'"))
+}
+}
diff --git a/man/get_result_tree.Rd b/man/get_result_tree.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..782f33d5c18be16e8eedec717e9158df4e7f7a47
--- /dev/null
+++ b/man/get_result_tree.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_result.R
+\name{get_result_tree}
+\alias{get_result_tree}
+\title{Get correspondence between network object and columns in result binary file}
+\usage{
+get_result_tree(cfg, scenario, variant = 0)
+}
+\arguments{
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+
+\item{scenario}{\link{numeric}, the scenario to read}
+
+\item{variant}{\link{numeric}, the variant to read}
+}
+\value{
+a \link{data.frame} with following columns:
+\itemize{
+\item "bf", "sn", "nd", "pr", "ouv": location of the result with number of respectively reach, section, node, offtake, and device.
+\item "var": the name of the calculated variable
+\item "col": the column number in the matrix produced by \link{read_bin_result_matrix}
+}
+}
+\description{
+Get correspondence between network object and columns in result binary file
+}
+\examples{
+\dontrun{
+cfg <- cfg_tmp_project()
+sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+df <- get_result_tree(cfg, 1)
+head(df)
+}
+}
diff --git a/man/merge_reaches.Rd b/man/merge_reaches.Rd
index fa030e3e039bb72077bbf7428055310b2a90845e..1ca02aa21a10fea5b1cb2d1ccae56a057a79cfae 100644
--- a/man/merge_reaches.Rd
+++ b/man/merge_reaches.Rd
@@ -2,18 +2,18 @@
% Please edit documentation in R/merge_reaches.R
\name{merge_reaches}
\alias{merge_reaches}
-\title{Merge several ReachTxt objects into one}
+\title{Merge several \emph{ReachTxt} objects into one}
\usage{
merge_reaches(...)
}
\arguments{
-\item{...}{ReachTxt objects}
+\item{...}{\emph{ReachTxt} objects}
}
\value{
-
+a \emph{ReachTxt} object (See \link{create_uniform_reach_txt} and \link{dem_to_reach}) containing the merged reaches.
}
\description{
-Merge several ReachTxt objects into one
+Merge several \emph{ReachTxt} objects into one
}
\examples{
# Minor bed generation
diff --git a/man/read_bin_result_matrix.Rd b/man/read_bin_result_matrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..c0e2bab1b2ad39de53b8c1c59b3849a4032ae552
--- /dev/null
+++ b/man/read_bin_result_matrix.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_result.R
+\name{read_bin_result_matrix}
+\alias{read_bin_result_matrix}
+\title{Read matrix of SIC simulation result file}
+\usage{
+read_bin_result_matrix(cfg, scenario, variant = 0)
+}
+\arguments{
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+
+\item{scenario}{\link{numeric}, the scenario to read}
+
+\item{variant}{\link{numeric}, the variant to read}
+}
+\value{
+\link{matrix} with the simulation results
+}
+\description{
+Read matrix of SIC simulation result file
+}
+\examples{
+\dontrun{
+cfg <- cfg_tmp_project()
+sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+m <- read_bin_result_matrix(cfg, 1)
+str(m)
+}
+}
diff --git a/man/sic_import_reaches.Rd b/man/sic_import_reaches.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..711ba97909dbc08e63b1572d6cb7c3cfa2938a9e
--- /dev/null
+++ b/man/sic_import_reaches.Rd
@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sic_import_reaches.R
+\name{sic_import_reaches}
+\alias{sic_import_reaches}
+\title{Import reach geometries into a SIC project}
+\usage{
+sic_import_reaches(
+ reaches,
+ import_mode = "ImportXml_UPDATE",
+ cfg = loadConfig()
+)
+}
+\arguments{
+\item{reaches}{A \link{list} of ReachTxt objects (See \link{split_reach})}
+
+\item{import_mode}{\link{character}, importation mode of EdiSIC (See \url{https://sic.g-eau.fr/Import-sections-in-text-format?lang=en#import-modes-2})}
+
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+}
+\value{
+A \link{numeric} code returned by \link{shell}
+}
+\description{
+Import reach geometries into a SIC project
+}
+\examples{
+# Minor bed generation
+profT <- matrix(c(2, 6, 0, 2), ncol = 2)
+min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+ upstream_bed_elevation = 8 + 10000 * 0.002,
+ slope = 0.002,
+ section_type = "L",
+ profile = profT)
+
+# Major bed generation
+data("floodam_ead_dem")
+dem <- terra::rast(floodam_ead_dem)
+node_coords <- matrix(c(102550, 102550, 110000, 100000), ncol = 2)
+space_step = 100
+section_width = 5000
+maj_reach <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+
+# Merge minor and major beds and split into 2 reaches
+reach <- merge_reaches(min_reach, maj_reach)
+reaches <- split_reach(reach, seq(0, 10000, 5000))
+
+\dontrun{
+# Import with EdiSic
+cfg <- cfg_tmp_project()
+sic_import_reaches(reaches, cfg = cfg)
+}
+}
diff --git a/man/sic_run_fortran.Rd b/man/sic_run_fortran.Rd
index 3ed6001297e9ebb0d986bd042dcb6642be878bb4..0c972bbded282694e097bedd9dc105ca2b1b6bd2 100644
--- a/man/sic_run_fortran.Rd
+++ b/man/sic_run_fortran.Rd
@@ -14,7 +14,7 @@ sic_run_fortran(prog, params = list(), cfg = loadConfig())
\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
}
\value{
-
+Error code returned by \link{shell}.
}
\description{
Run Talweg, Fluvia or Sirene
@@ -26,7 +26,8 @@ If argument \code{params} is a \link{list}, arguments are injected in the comman
\examples{
\dontrun{
# Run steady simulation for the scenario #1
+cfg <- cfg_tmp_project()
params <- list(SCE=1)
-sic_run_fortran("fluvia", params)
+sic_run_fortran("fluvia", params, cfg = cfg)
}
}
diff --git a/tests/testthat/helper-sic_local_config.R b/tests/testthat/helper-sic_local_config.R
deleted file mode 100644
index 30370f940bb0f8edd5b2d67b59b95d8ac543cee6..0000000000000000000000000000000000000000
--- a/tests/testthat/helper-sic_local_config.R
+++ /dev/null
@@ -1,8 +0,0 @@
-# Set local configuration for SIC tests
-loadLocalConfig <- function() {
- xml_path <- tempfile("sic_project", fileext = ".xml")
- file.copy(system.file("sic_project_test1.xml", package = "rsic2"),
- xml_path,
- overwrite = TRUE)
- loadConfig(xml_path = xml_path)
-}
diff --git a/tests/testthat/test-create_uniform_reach_txt.R b/tests/testthat/test-create_uniform_reach_txt.R
index c6eaa3442adbd6652aab15dba749d70d8e739500..62a8c12785421b8ee16bd432599cf6921c53ee41 100644
--- a/tests/testthat/test-create_uniform_reach_txt.R
+++ b/tests/testthat/test-create_uniform_reach_txt.R
@@ -6,15 +6,18 @@ profT <- list(
)
test_that("Trapezoidal minor section", {
+ profT2 <- profT
+ profT2$ZF <- 99
+ profT2$ZB <- 101
expect_equal(
create_uniform_reach_txt(abscissas = c(1000, 2000),
upstream_bed_elevation = 100,
slope = 0.001,
section_type = "T",
- profile = profT),
+ profile = profT)[1:2],
list(
- "00001000" = c("Section x=1000 $ 1000 $ $ 0 $ T", "2\t1", "102\t100"),
- "00002000" = c("Section x=2000 $ 2000 $ $ 0 $ T", "2\t1", "101\t99")
+ "00001000" = create_section_txt("Section x=1000", 1000, "T", profT),
+ "00002000" = create_section_txt("Section x=2000", 2000, "T", profT2)
)
)
})
diff --git a/tests/testthat/test-get_result.R b/tests/testthat/test-get_result.R
new file mode 100644
index 0000000000000000000000000000000000000000..cbe939ddd9679d0a2f93ccab4a7216de527ff526
--- /dev/null
+++ b/tests/testthat/test-get_result.R
@@ -0,0 +1,11 @@
+skip_on_ci()
+
+cfg <- cfg_tmp_project()
+sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+
+test_that("get_result returns a matrix with correct colnames", {
+ result <- get_result(cfg, 1, filters = c("bf=4", "var='Z'"))
+ expect_true(is.matrix(result))
+ expect_type(result, "double")
+ expect_equal(colnames(result), sprintf("bf:4|sn:%d|var:Z", 1:4))
+})
diff --git a/tests/testthat/test-set_initial_conditions.R b/tests/testthat/test-set_initial_conditions.R
index d32e02c7eaec882f6f3ef1a4c840385a70137c73..4aad0fceb8c6999ae05d4a6a1642456841ed44fe 100644
--- a/tests/testthat/test-set_initial_conditions.R
+++ b/tests/testthat/test-set_initial_conditions.R
@@ -1,7 +1,7 @@
skip_on_ci()
test_that("set_initial_conditions works", {
- cfg <- loadLocalConfig()
+ cfg <- cfg_tmp_project()
sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
set_initial_conditions(c(1, 0, 0, 1, 1), cfg = cfg)
sic_run_fortran("sirene", list(SCE = 1, VAR = 1), cfg = cfg)
diff --git a/tests/testthat/test-sic_import_reaches.R b/tests/testthat/test-sic_import_reaches.R
index c12398ddea56a29fcce1add5a72099365cd29ddd..d0ea19db98f1a3ed811f28322a3cfb0112d423e7 100644
--- a/tests/testthat/test-sic_import_reaches.R
+++ b/tests/testthat/test-sic_import_reaches.R
@@ -1,6 +1,6 @@
skip_on_ci()
-cfg <- loadLocalConfig()
+cfg <- cfg_tmp_project()
# Minor bed generation
profT <- matrix(c(2, 6, 0, 2), ncol = 2)
@@ -23,5 +23,5 @@ reach <- merge_reaches(min_reach, maj_reach)
reaches <- split_reach(reach, seq(0, 10000, 5000))
test_that("Geometry Import works", {
- sic_import_reaches(reaches, cfg = cfg)
+ expect_equal(sic_import_reaches(reaches, cfg = cfg), 0)
})
diff --git a/tests/testthat/test-sic_run_export.R b/tests/testthat/test-sic_run_export.R
index 45e6a50d82e1d3097ece670d28e54d6d7260e69c..f7e8598bd5f83e7184e2f60cf1e149a75c10939f 100644
--- a/tests/testthat/test-sic_run_export.R
+++ b/tests/testthat/test-sic_run_export.R
@@ -1,6 +1,6 @@
skip_on_ci()
-cfg <- loadLocalConfig()
+cfg <- cfg_tmp_project()
test_that("RunExport on Fluvia run works", {
sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
diff --git a/tests/testthat/test-sic_run_fortran.R b/tests/testthat/test-sic_run_fortran.R
index 7a0b3db214ea82201d43e08b2f9bb3b8b73bc8f0..5d811fef85209aee370b3708df3895acf2225dc6 100644
--- a/tests/testthat/test-sic_run_fortran.R
+++ b/tests/testthat/test-sic_run_fortran.R
@@ -1,6 +1,6 @@
skip_on_ci()
-cfg <- loadLocalConfig()
+cfg <- cfg_tmp_project()
test_that("fluvia on SCE=1 should create a binary result file", {
sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)