ccp4: download via wget --continue in custom prep

Builtin curl in default prep has no retry/resume: an interrupted 3.7 GB
download restarts from zero and leaves a partial file that prep reuses
silently. Custom pbuild::prep resumes with wget --continue and gates the
build on gzip -t, so a truncated tarball can neither be reused nor
require a full re-download. urls: dropped from config.yaml (unused with
custom prep); install untars straight from the distfiles cache instead
of a pointless 3.7 GB copy via SRC_DIR.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

ccp4/README.md

@@ -3,9 +3,10 @@
 CCP4 suite (binary distribution, bundled with SHELX and ARP/wARP) for
 macromolecular crystallography. https://www.ccp4.ac.uk/
 
-- Vendor tarball install: default `prep` downloads the ~5 GB tarball
-  (cached in `$PMODULES_DISTFILESDIR`), `install` untars it into `$PREFIX`
-  and runs `BINARY.setup`.
+- Vendor tarball install: custom `prep` downloads the ~3.7 GB tarball with
+  `wget --continue` (resumes partial downloads; the builtin curl can't) and
+  verifies it with `gzip -t`; `install` untars it into `$PREFIX` and runs
+  `BINARY.setup`.
 - Non-interactive: the CCP4 licence is pre-agreed via `.agree2ccp4v6`
   before `BINARY.setup` runs, so the build never prompts.
 - No `shasums:`: the download link is session-gated (`sid=` expires), so
@@ -47,16 +48,12 @@ hand-downloaded tarball into the distfiles dir under the `name:` given in
 - **"done" but broken install**: modbuild has no errexit in hooks — errors in
   `pbuild::install` used to scroll by and the build still reported done. The
   build script now `std::die`s on every critical step.
-- **Truncated download reused silently**: an interrupted `curl` leaves a
-  partial file in the distfiles dir, and prep reuses any file it finds there
-  (no integrity check without `shasums:`). Symptom:
-  `gzip: stdin: unexpected end of file`. Fix:
-  ```bash
-  rm ~/.cache/Pmodules/distfiles/ccp4-9.0-shelx-arp-x86_64.tar.gz
-  modbuild build --clean-install 9.0
-  # or verify by hand before building:
-  gzip -t ~/.cache/Pmodules/distfiles/ccp4-9.0-shelx-arp-x86_64.tar.gz
-  ```
+- **Interrupted download**: prep now detects a truncated tarball with
+  `gzip -t` and resumes it with `wget --continue` — just re-run
+  `modbuild build 9.0`. A download that dies with
+  `Failure writing output to destination` means quota/disk full at the
+  distfiles dir, not a network problem — free space or move `download_dir:`
+  (see above) before retrying.
 - The tarball unpacks to `ccp4-9` (not `ccp4-9.0` as the CCP4 install doc
   implies); the build globs `ccp4-*/` instead of assuming the name.
 

ccp4/build

@@ -1,9 +1,25 @@
 #!/usr/bin/env modbuild
 
-# Download happens in the default prep via urls: in files/config.yaml.
-# unpacker: none because BINARY.setup patches paths relative to its final
-# location — we untar once, directly into $PREFIX, instead of unpacking
-# ~20 GB into the build tmp and copying it over.
+# Custom prep instead of urls: in config.yaml — modbuild's builtin curl has
+# no retry/resume, so an interrupted 3.7 GB download restarts from zero and
+# leaves a partial file the next prep reuses silently. wget --continue
+# resumes it, and gzip -t gates the build on an intact tarball.
+# sid= in the URL is session-generated on ccp4.ac.uk and expires; on download
+# failure get a fresh link from https://www.ccp4.ac.uk/download/ (package
+# "CCP4 + SHELX + ARP/wARP", Linux x86_64), or pre-stage the tarball by hand
+# in $PMODULES_DISTFILESDIR under the name below.
+pbuild::prep() {
+    local -r tarball="${PMODULES_DISTFILESDIR}/ccp4-${V}-shelx-arp-x86_64.tar.gz"
+    local -r url='https://www.ccp4.ac.uk/download/download_file.php?os=linux&pkg=ccp4-shelx-arp-x86_64&sid=09b78d1369f605f517efa393f88d2bae713ad0b6'
+    if ! gzip -t "${tarball}" 2>/dev/null; then
+        mkdir -p "${PMODULES_DISTFILESDIR}"
+        wget --continue --tries=20 --waitretry=30 \
+             --output-document="${tarball}" "${url}" || \
+            std::die 42 "ccp4: download failed — quota/disk full, or expired sid (fetch a fresh link from https://www.ccp4.ac.uk/download/)"
+        gzip -t "${tarball}" || \
+            std::die 42 "ccp4: tarball fails gzip -t after download — re-run to resume, or rm it to restart"
+    fi
+}
 
 pbuild::configure() {
     :
@@ -18,8 +34,10 @@ pbuild::install() {
     # modbuild has no errexit in hooks — without the die-guards a failed step
     # still ends in a "done" build with a broken PREFIX (happened 2026-08-18
     # with a truncated cached tarball).
-    tar -xzf "${SRC_DIR}/ccp4-${V}-shelx-arp-x86_64.tar.gz" || \
-        std::die 42 "ccp4: untar failed — cached tarball likely truncated; rm it from the distfiles dir and re-run (fetch a fresh sid link if the download fails)"
+    # untar straight from the distfiles cache — no point copying 3.7 GB into
+    # SRC_DIR first (prep already verified it with gzip -t)
+    tar -xzf "${PMODULES_DISTFILESDIR}/ccp4-${V}-shelx-arp-x86_64.tar.gz" || \
+        std::die 42 "ccp4: untar failed — rm the tarball from the distfiles dir and re-run"
     # the 9-series tarball unpacks to ccp4-9 (NOT ccp4-9.0 as the install doc
     # implies) — glob instead of guessing the name
     local -a top=( ccp4-*/ )

ccp4/files/config.yaml

@@ -5,14 +5,9 @@ ccp4:
     group: MX
     overlay: base
     relstage: unstable
-    urls:
-      # sid= is session-generated on ccp4.ac.uk and expires; if the download
-      # fails, get a fresh link from https://www.ccp4.ac.uk/download/
-      # (package "CCP4 + SHELX + ARP/wARP", Linux x86_64) or pre-stage the
-      # tarball as $PMODULES_DISTFILESDIR/ccp4-<version>-shelx-arp-x86_64.tar.gz
-      - url: "https://www.ccp4.ac.uk/download/download_file.php?os=linux&pkg=ccp4-shelx-arp-x86_64&sid=09b78d1369f605f517efa393f88d2bae713ad0b6"
-        name: ccp4-${V}-shelx-arp-x86_64.tar.gz
-        unpacker: none
+    # no urls: — download lives in build's pbuild::prep (wget --continue +
+    # gzip -t), because the builtin curl has no retry/resume for the 3.7 GB
+    # session-gated tarball
   versions:
     9.0:
       config: