Add available_sys method (#47)

* add available_sys method + dnf backend
* add test
* implement apt backend
* implement alpm backend
* update NEWS

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bspm
 Type: Package
 Title: Bridge to System Package Manager
-Version: 0.3.10
+Version: 0.3.10.1
 Authors@R: c(
     person("Iñaki", "Ucar", email="iucar@fedoraproject.org",
       role=c("aut", "cph", "cre"), comment=c(ORCID="0000-0001-6403-5550")))

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(available_sys)
 export(disable)
 export(discover)
 export(enable)

NEWS.md

@@ -1,3 +1,8 @@
+# bspm 0.3.10.1
+
+- New function `available_sys()` returns a matrix of available packages with
+  `"Package"`, `"Version"`, and `"Repository"` (#47 addressing #41).
+
 # bspm 0.3.10
 
 - Check backend availability on `enable()`, and trigger a warning if the

R/bridge.R

@@ -42,16 +42,16 @@ backend_check <- function() {
 
 backend_call <- function(method, pkgs=NULL) {
   if (root())
-    return(invisible(root_call(method, pkgs)))
+    return(root_call(method, pkgs))
 
   if (sudo_preferred())
-    return(invisible(sudo_call(method, pkgs, force=TRUE)))
+    return(sudo_call(method, pkgs, force=TRUE))
 
   if (dbus_service_alive())
-    return(invisible(dbus_call(method, pkgs)))
+    return(dbus_call(method, pkgs))
 
   if (interactive())
-    return(invisible(sudo_call(method, pkgs)))
+    return(sudo_call(method, pkgs))
 
   stop("cannot connect to the system package manager", call.=FALSE)
 }
@@ -71,9 +71,9 @@ root_call <- function(method, pkgs=NULL, sudo=NULL) {
   on.exit(unlink(tmp2, recursive=TRUE, force=TRUE))
 
   cmd <- system.file("service/bspm.py", package="bspm")
-  args <- method
+  args <- c(method, "-o", tmp)
   if (!is.null(pkgs))
-    args <- c(args, "-o", tmp, pkgs)
+    args <- c(args, pkgs)
   if (!is.null(sudo)) {
     args <- c(cmd, args)
     cmd <- sudo
@@ -104,6 +104,7 @@ dbus_call <- function(method, pkgs=NULL) {
   args <- c("call", "--timeout=1h", BUS_NAME, OPATH, IFACE, method)
   if (!is.null(pkgs))
     args <- c(args, "ias", Sys.getpid(), length(pkgs), pkgs)
+  else args <- c(args, "i", Sys.getpid())
   out <- system2nowarn(cmd, args, stdout=TRUE, stderr=TRUE)
 
   if (!length(out))

R/manager.R

@@ -39,6 +39,9 @@
 #'
 #' # now remove it
 #' bspm::remove_sys("units")
+#'
+#' # get available packages
+#' bspm::available_sys()
 #' }
 #'
 #' @name manager
@@ -50,12 +53,31 @@ install_sys <- function(pkgs) {
     deps <- unique(unlist(deps, use.names=FALSE))
     if (length(deps)) backend_call("install", deps)
   }
-  not.avail
+  invisible(not.avail)
 }
 
 #' @name manager
 #' @export
-remove_sys <- function(pkgs) backend_call("remove", pkgs)
+remove_sys <- function(pkgs) invisible(backend_call("remove", pkgs))
+
+#' @return Function \code{available_sys} returns a matrix with one row per
+#' package. Row names are the package names, and column names include
+#' \code{"Package"}, \code{"Version"}, \code{"Repository"}.
+#'
+#' @name manager
+#' @export
+available_sys <- function() {
+  pkgs <- do.call(rbind, strsplit(backend_call("available"), ";"))
+  colnames(pkgs) <- c("Package", "Version", "Repository")
+
+  vers <- package_version(pkgs[, "Version"])
+  pkgs <- pkgs[order(pkgs[, "Package"], vers, decreasing=TRUE), ]
+  pkgs <- pkgs[!duplicated(pkgs[, "Package"]), ]
+  pkgs <- pkgs[order(pkgs[, "Package"]), ]
+
+  rownames(pkgs) <- pkgs[, 1]
+  pkgs
+}
 
 #' @details The \code{discover} method is only needed when e.g. a new repository
 #' is added that contains packages with different prefixes (for example, your
@@ -66,4 +88,4 @@ remove_sys <- function(pkgs) backend_call("remove", pkgs)
 #'
 #' @name manager
 #' @export
-discover <- function() backend_call("discover")
+discover <- function() invisible(backend_call("discover"))

README.md

@@ -170,6 +170,7 @@ New backends for other package managers can be added to `inst/service/backend`.
 Each backend must implement the following functions:
 
 - `def discover() -> dict({ "prefixes" : list, "exclusions" : list })`
+- `def available(prefixes : list, exclusions : list) -> list`
 - `def install(prefixes : list, pkgs : list, exclusions : list) -> list`
 - `def remove(prefixes : list, pkgs : list, exclusions : list) -> list`
 

inst/service/backend/__init__.py

@@ -1,5 +1,5 @@
 libnames = ["dnf", "apt", "alpm"]
-attrs = ["discover", "install", "remove"]
+attrs = ["discover", "available", "install", "remove"]
 
 for libname in libnames:
     try:

inst/service/backend/_utils.py

@@ -1,7 +1,7 @@
 from contextlib import suppress
 from pathlib import Path
 from os import path
-import time
+import time, re
 
 CACHE_INVALIDATION_TIME = 5 # minutes
 
@@ -32,3 +32,23 @@ def cache_update(method, force=False):
     if force or time.time() - cache_time > CACHE_INVALIDATION_TIME * 60:
         method()
         Path(cache_file).touch()
+
+def pkg_strip(prefixes, name):
+    for prefix in sorted(prefixes, reverse=True):
+        name = name.replace(prefix, "")
+    return name
+
+def ver_strip(version):
+    version = list(reversed(version.split(":", 1)))[0]
+    version = version.rsplit("-", 1)[0]
+    version = version.rsplit("+")[0]
+    # remove things like .r79, see r-cran-rniftilib
+    version = re.sub("\.r[0-9]+$", "", version)
+    return version
+
+def pkg_record(prefixes, name, version, repo):
+    return ";".join([
+        pkg_strip(prefixes, name),
+        ver_strip(version),
+        repo.replace(" ", "_")
+    ])

inst/service/backend/alpm.py

@@ -1,4 +1,4 @@
-from ._utils import mark
+from ._utils import mark, pkg_record
 from functools import partial
 import pycman
 
@@ -12,29 +12,39 @@ def discover():
         "exclusions": []
     }
 
-def _cb_dl(filename, tx, total):
-    global _db_sync, _target
-    if _db_sync:
-        if tx == 3:
-            print(" %s" % filename.split(".")[0])
-    else:
-        if filename != _target:
-            _target = filename
-            print(" %s" % filename.split(".pkg.")[0])
-
-def _cb_event(id, msg):
-    global _target
-    if id == 9:
-        print(":: Processing package changes...")
-    elif id == 21:
-        _target = None
-        print(":: Retrieving packages...")
-
-def _cb_progress(target, percent, n, i):
-    global _target
-    if len(target) > 0 and target != _target:
-        _target = target
-        print("(%d/%d) %s" % (i, n, target))
+def _get_handle():
+    def _cb_dl(filename, tx, total):
+        global _db_sync, _target
+        if _db_sync:
+            if tx == 3:
+                print(" %s" % filename.split(".")[0])
+        else:
+            if filename != _target:
+                _target = filename
+                print(" %s" % filename.split(".pkg.")[0])
+
+    def _cb_event(id, msg):
+        global _target
+        if id == 9:
+            print(":: Processing package changes...")
+        elif id == 21:
+            _target = None
+            print(":: Retrieving packages...")
+
+    def _cb_progress(target, percent, n, i):
+        global _target
+        if len(target) > 0 and target != _target:
+            _target = target
+            print("(%d/%d) %s" % (i, n, target))
+
+    args = pycman.action_sync.parse_options([])
+    handle = pycman.config.init_with_config_and_options(args)
+
+    handle.dlcb = _cb_dl
+    handle.eventcb = _cb_event
+    handle.progresscb = _cb_progress
+
+    return handle
 
 def _update(handle):
     global _db_sync
@@ -52,28 +62,42 @@ def _remove(handle, t, repos, name):
     pkg = handle.get_localdb().get_pkg(name)
     t.remove_pkg(pkg)
 
+def available(prefixes, exclusions):
+    handle = _get_handle()
+
+    q = []
+    for db in handle.get_syncdbs():
+        for prefix in prefixes:
+            q += [_ for _ in db.search(prefix) if _.name.startswith(prefix)]
+    pkgs = []
+    for pkg in q:
+        if pkg.name in exclusions:
+            continue
+        pkgs.append(pkg_record(
+            prefixes,
+            pkg.name,
+            pkg.version,
+            pkg.db.name
+        ))
+
+    return pkgs
+
 def operation(op, prefixes, pkgs, exclusions):
-    args = pycman.action_sync.parse_options([])
-    handle = pycman.config.init_with_config_and_options(args)
-
-    handle.dlcb = _cb_dl
-    handle.eventcb = _cb_event
-    handle.progresscb = _cb_progress
-
+    handle = _get_handle()
     repos = dict((db.name, db) for db in handle.get_syncdbs())
     t = handle.init_transaction()
     _update(handle)
-    
+
     fun = partial(op, handle, t, repos)
     notavail = mark(fun, prefixes, pkgs, exclusions, trans="lower")
-    
+
     try:
         t.prepare()
         t.commit()
     except:
         pass
     t.release()
-    
+
     return notavail
 
 def install(prefixes, pkgs, exclusions):

inst/service/backend/apt.py

@@ -1,4 +1,4 @@
-from ._utils import mark, cache_update
+from ._utils import mark, cache_update, pkg_record
 from functools import partial
 import re
 import apt
@@ -14,32 +14,57 @@ def discover():
     cache = apt.Cache()
     cache_update(partial(cache.update, aprogress), force=True)
     cache.open()
+
     pkgs = [x for x in cache.keys() if re.match("^r-(.*)-(.*)", x)]
     prefixes = {"-".join(x.split("-")[0:2]) + "-" for x in pkgs}
-
+
+    cache.close()
+
     return {
         "prefixes": list(prefixes - {"r-doc-", "r-base-"}),
         "exclusions": []
     }
 
+def available(prefixes, exclusions):
+    aprogress = apt.progress.text.AcquireProgress()
+    cache = apt.Cache()
+    cache_update(partial(cache.update, aprogress))
+    cache.open()
+
+    q = [x for x in cache.keys() if re.match("|".join(prefixes), x)]
+    pkgs = []
+    for pkg in q:
+        if pkg in exclusions:
+            continue
+        pkgs.append(pkg_record(
+            prefixes,
+            cache[pkg].candidate.source_name,
+            cache[pkg].candidate.version,
+            cache[pkg].candidate.origins[0].origin
+        ))
+
+    cache.close()
+
+    return pkgs
+
 def operation(op, prefixes, pkgs, exclusions):
     def cc(cache, method):
         def wrapper(pkgname):
             getattr(cache[pkgname], "mark_" + method)()
         return wrapper
-    
+
     oprogress = apt.progress.text.OpProgress()
     aprogress = apt.progress.text.AcquireProgress()
-    
+
     cache = apt.Cache(oprogress)
     cache_update(partial(cache.update, aprogress))
     cache.open(oprogress)
-    
+
     notavail = mark(cc(cache, op), prefixes, pkgs, exclusions, trans="lower")
-    
+
     cache.commit(aprogress)
     cache.close()
-    
+
     return notavail
 
 def install(prefixes, pkgs, exclusions):