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breaking change how (sub)project command initialization works
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Subprojects have to now explicitly define an initCommands function that
registers the projects commands with registerCommands.

This allows for subprojects to exist on multiple levels,
e.g. to make a sub-project of Foldseek.

your_tool.cpp needs to include now something as follows:

std::vector<Command> yourToolCommands = {
    ...
};

extern std::vector<Command> baseCommands;
void init() {
    registerCommands(&baseCommands);
    registerCommands(&yourToolCommands);
}
void (*initCommands)(void) = init;

instead of:
std::vector<Command> commands = {
    ...
}
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@milot-mirdita
milot-mirdita committed Nov 19, 2023
1 parent 9b9383a commit 1c08685
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Showing 5 changed files with 88 additions and 97 deletions.
14 changes: 9 additions & 5 deletions cmake/MMseqsSetupDerivedTarget.cmake
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Original file line number Diff line number Diff line change
@@ -1,12 +1,16 @@
include(AppendTargetProperty)

function (mmseqs_setup_derived_target TARGET)
get_target_property(COMPILE_TMP mmseqs-framework COMPILE_FLAGS)
get_target_property(LINK_TMP mmseqs-framework LINK_FLAGS)
get_target_property(DEF_TMP mmseqs-framework COMPILE_DEFINITIONS)
get_target_property(INCL_TMP mmseqs-framework INCLUDE_DIRECTORIES)
set(SOURCE "${ARGN}")
if(NOT SOURCE)
set(SOURCE "mmseqs-framework")
endif()
get_target_property(COMPILE_TMP ${SOURCE} COMPILE_FLAGS)
get_target_property(LINK_TMP ${SOURCE} LINK_FLAGS)
get_target_property(DEF_TMP ${SOURCE} COMPILE_DEFINITIONS)
get_target_property(INCL_TMP ${SOURCE} INCLUDE_DIRECTORIES)

target_link_libraries(${TARGET} mmseqs-framework)
target_link_libraries(${TARGET} ${SOURCE})
append_target_property(${TARGET} COMPILE_FLAGS ${COMPILE_TMP})
append_target_property(${TARGET} LINK_FLAGS ${LINK_TMP})
set_property(TARGET ${TARGET} APPEND PROPERTY COMPILE_DEFINITIONS ${DEF_TMP})
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156 changes: 65 additions & 91 deletions src/commons/Application.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -16,31 +16,30 @@ extern const char *show_extended_help;
extern const char *show_bash_info;
extern bool hide_base_commands;

extern std::vector<Command> commands;
extern std::vector<Command> baseCommands;
extern std::vector<std::vector<Command>*> commands;
extern std::vector<Categories> categories;
extern void (*validatorUpdate)(void);
extern void (*initCommands)(void);

Command *getCommandByName(const char *s) {
for (size_t i = 0; i < commands.size(); i++) {
Command &p = commands[i];
if (!strcmp(s, p.cmd))
return &p;
}

const Command* getCommandByName(const char *s) {
// allow base commands also to be called with a prefix, e.g. "mmseqs base:createdb"
// this allows inheriting programs to find shadowed base modules
const char *prefix = "base:";
const char *check = strncmp(s, prefix, strlen(prefix)) == 0 ? s + strlen(prefix) : s;
for (size_t i = 0; i < baseCommands.size(); i++) {
Command &p = baseCommands[i];
if (!strcmp(check, p.cmd))
return &p;

for (size_t i = 0; i < commands.size(); i++) {
for (size_t j = 0; j < commands[i]->size(); j++) {
const Command &p = (*commands[i])[j];
if (!strcmp(s, p.cmd))
return &p;
if (i == 0 && !strcmp(check, p.cmd))
return &p;
}
}
return NULL;
}

int runCommand(Command *p, int argc, const char **argv) {
int runCommand(const Command *p, int argc, const char **argv) {
Timer timer;
int status = p->commandFunction(argc, argv, *p);
Debug(Debug::INFO) << "Time for processing: " << timer.lap() << "\n";
Expand All @@ -57,21 +56,17 @@ void printUsage(bool showExtended) {

std::vector<int> showCategoryHeader(categories.size(), 0);
for (size_t i = 0; i < categories.size(); ++i) {
for (size_t j = 0; j < commands.size(); j++) {
Command &p = commands[j];
if (p.mode & categories[i].mode) {
showCategoryHeader[i] = 1;
break;
}
}
size_t start = 0;
if (hide_base_commands) {
continue;
}
for (size_t j = 0; j < baseCommands.size(); j++) {
Command &p = baseCommands[j];
if (p.mode & categories[i].mode) {
showCategoryHeader[i] = 1;
break;
start = commands.size() - 1;
}
for (size_t j = start; j < commands.size(); j++) {
for (size_t k = 0; k < commands[j]->size(); k++) {
const Command &p = (*commands[j])[k];
if (p.mode & categories[i].mode) {
showCategoryHeader[i] = 1;
break;
}
}
}
}
Expand All @@ -93,24 +88,18 @@ void printUsage(bool showExtended) {

usage << "\n" << std::setw(20) << categories[i].title << "\n";
for (size_t j = 0; j < commands.size(); j++) {
struct Command &p = commands[j];
if (showExtended == false && (p.mode & COMMAND_EXPERT) != 0) {
continue;
}
if (p.mode & categories[i].mode) {
usage << std::left << std::setw(20) << " " + std::string(p.cmd) << "\t" << p.description << "\n";
size_t start = 0;
if (hide_base_commands) {
start = commands.size() - 1;
}
}
if (hide_base_commands) {
continue;
}
for (size_t j = 0; j < baseCommands.size(); j++) {
struct Command &p = baseCommands[j];
if (showExtended == false && (p.mode & COMMAND_EXPERT) != 0) {
continue;
}
if (p.mode & categories[i].mode) {
usage << std::left << std::setw(20) << " " + std::string(p.cmd) << "\t" << p.description << "\n";
for (size_t k = start; k < commands[j]->size(); k++) {
const Command &p = (*commands[j])[k];
if (showExtended == false && (p.mode & COMMAND_EXPERT) != 0) {
continue;
}
if (p.mode & categories[i].mode) {
usage << std::left << std::setw(20) << " " + std::string(p.cmd) << "\t" << p.description << "\n";
}
}
}
}
Expand All @@ -130,14 +119,12 @@ int shellcompletion(int argc, const char **argv) {
// mmseqs programs
if (argc == 0) {
for (size_t i = 0; i < commands.size(); i++) {
struct Command &p = commands[i];
if (p.mode & COMMAND_HIDDEN)
continue;
Debug(Debug::INFO) << p.cmd << " ";
}
if (hide_base_commands == false) {
for (size_t i = 0; i < baseCommands.size(); i++) {
struct Command &p = baseCommands[i];
size_t start = 0;
if (hide_base_commands) {
start = commands.size() - 1;
}
for (size_t j = start; j < commands[i]->size(); j++) {
const Command &p = (*commands[i])[j];
if (p.mode & COMMAND_HIDDEN)
continue;
Debug(Debug::INFO) << p.cmd << " ";
Expand All @@ -149,30 +136,19 @@ int shellcompletion(int argc, const char **argv) {
// mmseqs parameters for given program
if (argc == 1) {
for (size_t i = 0; i < commands.size(); i++) {
struct Command &p = commands[i];
if (strcmp(p.cmd, argv[0]) != 0) {
continue;
}
if (p.params == NULL) {
continue;
size_t start = 0;
if (hide_base_commands) {
start = commands.size() - 1;
}
for (std::vector<MMseqsParameter *>::const_iterator it = p.params->begin(); it != p.params->end(); ++it) {
Debug(Debug::INFO) << (*it)->name << " ";
}
Debug(Debug::INFO) << "\n";
break;
}
if (hide_base_commands == false) {
for (size_t i = 0; i < baseCommands.size(); i++) {
struct Command &p = baseCommands[i];
for (size_t j = start; j < commands[i]->size(); j++) {
const Command &p = (*commands[i])[j];
if (strcmp(p.cmd, argv[0]) != 0) {
continue;
}
if (p.params == NULL) {
continue;
}
for (std::vector<MMseqsParameter *>::const_iterator it = p.params->begin();
it != p.params->end(); ++it) {
for (std::vector<MMseqsParameter *>::const_iterator it = p.params->begin(); it != p.params->end(); ++it) {
Debug(Debug::INFO) << (*it)->name << " ";
}
Debug(Debug::INFO) << "\n";
Expand All @@ -185,6 +161,10 @@ int shellcompletion(int argc, const char **argv) {
}

int main(int argc, const char **argv) {
if (initCommands != NULL) {
initCommands();
}

if (argc < 2) {
printUsage(false);
return EXIT_SUCCESS;
Expand All @@ -201,7 +181,7 @@ int main(int argc, const char **argv) {
FileUtil::fixRlimitNoFile();

setenv("MMSEQS", argv[0], true);
Command *c = NULL;
const Command *c = NULL;
if (strncmp(argv[1], "shellcompletion", strlen("shellcompletion")) == 0) {
return shellcompletion(argc - 2, argv + 2);
} else if ((c = getCommandByName(argv[1])) != NULL) {
Expand All @@ -211,37 +191,31 @@ int main(int argc, const char **argv) {
Debug(Debug::INFO) << "\nInvalid Command: " << argv[1] << "\n";

// Suggest some command that the user might have meant
size_t index = SIZE_MAX;
size_t indexI = SIZE_MAX;
size_t indexJ = SIZE_MAX;
int maxDistance = 0;
for (size_t i = 0; i < commands.size(); ++i) {
struct Command &p = commands[i];
if (p.mode & COMMAND_HIDDEN) {
continue;
}

int distance = DistanceCalculator::localLevenshteinDistance(argv[1], p.cmd);
if (distance > maxDistance) {
maxDistance = distance;
index = i;
for (size_t i = 0; i < commands.size(); i++) {
size_t start = 0;
if (hide_base_commands) {
start = commands.size() - 1;
}
}

if (hide_base_commands == false) {
for (size_t i = 0; i < baseCommands.size(); ++i) {
struct Command &p = baseCommands[i];
if (p.mode & COMMAND_HIDDEN)
for (size_t j = start; j < commands[i]->size(); j++) {
const Command &p = (*commands[i])[j];
if (p.mode & COMMAND_HIDDEN) {
continue;
}

int distance = DistanceCalculator::localLevenshteinDistance(argv[1], p.cmd);
if (distance > maxDistance) {
maxDistance = distance;
index = i;
indexI = i;
indexJ = j;
}
}
}

if (index != SIZE_MAX) {
Debug(Debug::WARNING) << "Did you mean \"" << argv[0] << " " << baseCommands[index].cmd << "\"?\n";
if (indexI != SIZE_MAX && indexJ != SIZE_MAX) {
Debug(Debug::WARNING) << "Did you mean \"" << argv[0] << " " << (*commands[indexI])[indexJ].cmd << "\"?\n";
}

return EXIT_FAILURE;
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5 changes: 5 additions & 0 deletions src/commons/Command.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
#include "Command.h"
#include "Parameters.h"

std::vector<std::vector<Command>*> commands;
void registerCommands(std::vector<Command>* cmd) {
commands.emplace_back(cmd);
}

std::vector<Categories> categories = {
{"Easy workflows for plain text input/output", COMMAND_EASY},
{"Main workflows for database input/output", COMMAND_MAIN},
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2 changes: 2 additions & 0 deletions src/commons/Command.h
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Original file line number Diff line number Diff line change
Expand Up @@ -108,4 +108,6 @@ struct Categories {
CommandMode mode;
};

void registerCommands(std::vector<Command>* cmd);

#endif
8 changes: 7 additions & 1 deletion src/mmseqs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,13 @@ extern const char* MMSEQS_CURRENT_INDEX_VERSION;
const char* index_version_compatible = MMSEQS_CURRENT_INDEX_VERSION;
bool hide_base_commands = false;
void (*validatorUpdate)(void) = 0;
std::vector<Command> commands = {};

extern std::vector<Command> baseCommands;
void init() {
registerCommands(&baseCommands);
}
void (*initCommands)(void) = init;

std::vector<DatabaseDownload> externalDownloads = {};
std::vector<KmerThreshold> externalThreshold = {};

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